From 9400f26eeffb54e25456966fb4d9df5468d89712 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Fri, 6 Sep 2019 22:55:03 +0200 Subject: [PATCH 01/86] move ITs to tools/interactive (cherry picked from commit 1c5bc4f55a781e48e4fd6017e4e49a52db8c4657) --- interactivetool_askomics.xml | 59 ++++++++++++++++ interactivetool_bam_iobio.xml | 44 ++++++++++++ interactivetool_cellxgene.xml | 29 ++++++++ interactivetool_ethercalc.xml | 63 +++++++++++++++++ interactivetool_hicbrowser.xml | 33 +++++++++ interactivetool_jupyter_notebook.xml | 100 +++++++++++++++++++++++++++ interactivetool_neo4j.xml | 41 +++++++++++ interactivetool_phinch.xml | 37 ++++++++++ 8 files changed, 406 insertions(+) create mode 100644 interactivetool_askomics.xml create mode 100644 interactivetool_bam_iobio.xml create mode 100644 interactivetool_cellxgene.xml create mode 100644 interactivetool_ethercalc.xml create mode 100644 interactivetool_hicbrowser.xml create mode 100644 interactivetool_jupyter_notebook.xml create mode 100644 interactivetool_neo4j.xml create mode 100644 interactivetool_phinch.xml diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml new file mode 100644 index 00000000000..71c3fe9a437 --- /dev/null +++ b/interactivetool_askomics.xml @@ -0,0 +1,59 @@ + + AskOmics, a visual SPARQL query builder + + quay.io/askomics/askomics-ie:17.12_g19.09 + + + + 6543 + /login_api_gie?key=abcd + + + + ${__app__.config.galaxy_infrastructure_url} + + #if $__user__: + #for $api_key in $__user__.api_keys: + ${api_key.key} + #break + #end for + #end if + + + + + + + + + + + + + + AskOmics is a visual SPARQL query interface supporting both intuitive data integration and + querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL. + + diff --git a/interactivetool_bam_iobio.xml b/interactivetool_bam_iobio.xml new file mode 100644 index 00000000000..2f1c531861c --- /dev/null +++ b/interactivetool_bam_iobio.xml @@ -0,0 +1,44 @@ + + + qiaoy/iobio-bundle.bam-iobio:1.0-ondemand + + + + 80 + + + + /tmp/app.conf && + mv /tmp/app.conf /etc/supervisor.d/app.conf && + + /usr/bin/supervisord -c /etc/supervisord.conf + ]]> + + + + + + + + + + + BAM iobio visualisation. + + diff --git a/interactivetool_cellxgene.xml b/interactivetool_cellxgene.xml new file mode 100644 index 00000000000..546bd7ab58f --- /dev/null +++ b/interactivetool_cellxgene.xml @@ -0,0 +1,29 @@ + + + quay.io/galaxy/cellxgene-galaxy-ie:ie2 + + + + 80 + + + + + + + + + + + + + + Interactive tool for visualising AnnData. + + diff --git a/interactivetool_ethercalc.xml b/interactivetool_ethercalc.xml new file mode 100644 index 00000000000..88676c1e997 --- /dev/null +++ b/interactivetool_ethercalc.xml @@ -0,0 +1,63 @@ + + + shiltemann/ethercalc-galaxy-ie:17.05 + + + + 8000 + + + loading.txt + && + curl --include --request PUT --header "Content-Type: text/csv" --data-binary @loading.txt http://localhost:8000/_/galaxy + && + + ## remove dump file so this doesnt appear in audit trail + rm /dump.json + && + + ## load dataset into worksheet + curl --include --request PUT --header "Content-Type: text/csv" --data-binary @$infile http://localhost:8000/_/galaxy + && + + tail -f /etc/hosts + + ]]> + + + +&1) +while [[ \${STATUS} =~ "refused" ]] +do + echo "waiting for ethercalc: \$STATUS \n" + STATUS=\$(curl --include 'http://localhost:8000/_/galaxy' 2>&1) + sleep 2 +done + ]]> + + + + + + + + + + + + EtherCalc is a web spreadsheet. + https://ethercalc.net + + diff --git a/interactivetool_hicbrowser.xml b/interactivetool_hicbrowser.xml new file mode 100644 index 00000000000..7aaa8a3e8e7 --- /dev/null +++ b/interactivetool_hicbrowser.xml @@ -0,0 +1,33 @@ + + + bgruening/hicbrowser + + + + 80 + + + + + + + + + + + + + + Visualising HiC data with HiCBrowser. + + diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml new file mode 100644 index 00000000000..9dd3e36d3ee --- /dev/null +++ b/interactivetool_jupyter_notebook.xml @@ -0,0 +1,100 @@ + + + quay.io/bgruening/docker-jupyter-notebook:ie2 + + + + 8888 + ipython/tree + + + + ${__app__.security.encode_id($jupyter_notebook.history_id)} + ${__app__.config.galaxy_infrastructure_url} + 8080 + ${__app__.config.galaxy_infrastructure_url} + + #if $__user__: + #for $api_key in $__user__.api_keys: + ${api_key.key} + #break + #end for + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, + visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, + machine learning, and much more. + + Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to + do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter. + + You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset. + If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history. + + You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function. + + diff --git a/interactivetool_neo4j.xml b/interactivetool_neo4j.xml new file mode 100644 index 00000000000..0b31a8b303e --- /dev/null +++ b/interactivetool_neo4j.xml @@ -0,0 +1,41 @@ + + + quay.io/sanbi-sa/neo_ie:3.1.9 + + + + 80 + + + + + 2345 + 2345 + false + + + + + + + + + + + + + Neo4j is a highly scalable, robust native graph database. + + diff --git a/interactivetool_phinch.xml b/interactivetool_phinch.xml new file mode 100644 index 00000000000..d77c9274ad3 --- /dev/null +++ b/interactivetool_phinch.xml @@ -0,0 +1,37 @@ + + + shiltemann/docker-phinch-galaxy:16.04 + + + + 80 + + + &1 > /var/log/phinch.log + + ]]> + + + + + + + + + + + Interactive tool for visualising Biom data. + + From 2f67bb0f4d539b6f768edc635f01c207a5046947 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Fri, 6 Sep 2019 23:05:01 +0200 Subject: [PATCH 02/86] move default notebook as well (cherry picked from commit 6d8848e399446fdc3cb1e0c81b1e88c80b03c515) --- default_notebook.ipynb | 53 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 default_notebook.ipynb diff --git a/default_notebook.ipynb b/default_notebook.ipynb new file mode 100644 index 00000000000..e9573752478 --- /dev/null +++ b/default_notebook.ipynb @@ -0,0 +1,53 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Welcome to the interactive Galaxy IPython Notebook." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You can access your data via the dataset number. Using a Python kernel, you can access dataset number 42 with ``handle = open(get(42), 'r')``.\n", + "To save data, write your data to a file, and then call ``put('filename.txt')``. The dataset will then be available in your galaxy history.\n
", + "When using a non-Python kernel, ``get`` and ``put`` are available as command-line tools, which can be accessed using system calls in R, Julia, and Ruby. For example, to read dataset number 42 into R, you can write ```handle <- file(system('get -i 42', intern = TRUE))```.\n", + "To save data in R, write the data to a file and then call ``system('put -p filename.txt')``.\n", + "Notebooks can be saved to Galaxy by clicking the large green button at the top right of the IPython interface.
\n", + "More help and informations can be found on the project [website](https://github.com/bgruening/docker-jupyter-notebook)." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 2", + "language": "python", + "name": "python2" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.10" + } + }, + "nbformat": 4, + "nbformat_minor": 0 +} From 58a00bef9c035495f46a1a92ac73dbe7fe66751e Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Fri, 6 Sep 2019 23:07:39 +0200 Subject: [PATCH 03/86] improve description of Askomics (cherry picked from commit 1d4dc27e509a4084857fec63c20698d69979c8eb) --- interactivetool_askomics.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml index 71c3fe9a437..c1ce9d3bd11 100644 --- a/interactivetool_askomics.xml +++ b/interactivetool_askomics.xml @@ -1,5 +1,5 @@ - AskOmics, a visual SPARQL query builder + a visual SPARQL query builder quay.io/askomics/askomics-ie:17.12_g19.09 From 06bbc492e2faf0d7c7d53d0ac207f34ca3224e21 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 3 Oct 2019 13:40:33 +0200 Subject: [PATCH 04/86] move to right dir --- interactivetool_paraview.xml | 50 ++++++++++++++++++++++++++ interactivetool_rstudio.xml | 69 ++++++++++++++++++++++++++++++++++++ 2 files changed, 119 insertions(+) create mode 100644 interactivetool_paraview.xml create mode 100644 interactivetool_rstudio.xml diff --git a/interactivetool_paraview.xml b/interactivetool_paraview.xml new file mode 100644 index 00000000000..c801600ef0e --- /dev/null +++ b/interactivetool_paraview.xml @@ -0,0 +1,50 @@ + + + + bmcv/galaxy-paraviewweb:latest + + + + 8777 + + + + + localhost:8080 + wss + -dr,--mesa-swr + + + + + + + + + + + + + ParaView is an open-source, multi-platform application designed to visualize data sets of varying sizes from small to very large. + + diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml new file mode 100644 index 00000000000..30b55db7f11 --- /dev/null +++ b/interactivetool_rstudio.xml @@ -0,0 +1,69 @@ + + + quay.io/erasche/docker-rstudio-notebook:19.05 + + + + 80 + rstudio/ + + + + ${__app__.security.encode_id($jupyter_notebook.history_id)} + ${__app__.config.galaxy_infrastructure_url} + 8080 + ${__app__.config.galaxy_infrastructure_url} + + #if $__user__: + #for $api_key in $__user__.api_keys: + ${api_key.key} + #break + #end for + #end if + + + + + + + + + + + + + + + + + + + + This familiar R analysis software suite will let you explore your + datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr, + LaTeX, bioconductor, cummeRbund, and many more pre-installed packages. + + Galaxy offers you to use RStudio directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to + do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in RStudio. + + The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save(). + + For example, gx_get(42) will fetch dataset 42 from your history and return the file location + + From 6b0b5edbbfa092e9e51732d8e9ae931b22e197e2 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 5 Oct 2019 23:58:46 +0200 Subject: [PATCH 05/86] add wilson --- interactivetool_wilson.xml | 51 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 interactivetool_wilson.xml diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml new file mode 100644 index 00000000000..5ce1b73272f --- /dev/null +++ b/interactivetool_wilson.xml @@ -0,0 +1,51 @@ + + Webbased Interactive Omics visualization + + loosolab/wilson:2.1.0 + + + + 3838 + + + &1 + ]]> + + + + + + + + + + +`_ + +.. class:: infomark + +Wilson uses the CLARION file format, which is a generic file format for quantitative comparisons of high throughput screens. + +CLARION is a data format specially developed to be used with Wilson, which relies on a tab-delimited table with +a metadata header to describe the following columns. It is based on the Summarized Experiment format and supports +all types of data which can be reduced to features and their annotation (e.g. genes, transcripts, proteins, probes) +with assigned numerical values (e.g. count, score, log2foldchange, z-score, p-value). Most result tables derived from RNA-Seq, +ChIP/ATAC-Seq, Proteomics, Microarrays, and many other analyses can thus be easily reformatted to become compatible +without having to modify the code of Wilson for each specific experiment. + +Please check the following link for details considering the `CLARION format `_. + + + +]]> + + + 10.1093/bioinformatics/bty711 + + From 5df22293ef936aabe9d4b4c14e1afb88e2f77662 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 6 Oct 2019 00:01:57 +0200 Subject: [PATCH 06/86] deactivate monitor script --- interactivetool_rstudio.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml index 30b55db7f11..7454c973b85 100644 --- a/interactivetool_rstudio.xml +++ b/interactivetool_rstudio.xml @@ -36,6 +36,8 @@ ## change into the directory where the notebooks are located cd ./rstudio/ && + sed -i 's|/monitor.*||g' /etc/services.d/nginx/run && + /init ]]> From 73dd265703a1fa7b7c65be73aae22138f9fd2512 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 6 Oct 2019 00:48:50 +0200 Subject: [PATCH 07/86] fix tool id --- interactivetool_wilson.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml index 5ce1b73272f..9d724a0fbe5 100644 --- a/interactivetool_wilson.xml +++ b/interactivetool_wilson.xml @@ -1,4 +1,4 @@ - + Webbased Interactive Omics visualization loosolab/wilson:2.1.0 From c7f5136c8f7942312b2f83075b25e5ff847f9b82 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 8 Oct 2019 14:51:38 +0200 Subject: [PATCH 08/86] temporarily disable all input data --- interactivetool_rstudio.xml | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml index 7454c973b85..9f39f227348 100644 --- a/interactivetool_rstudio.xml +++ b/interactivetool_rstudio.xml @@ -28,11 +28,6 @@ mkdir -p ./rstudio/outputs/ && mkdir -p ./rstudio/data && - #if $input: - #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier)) - ln -sf '$input' './rstudio/data/${cleaned_name}' && - #end if - ## change into the directory where the notebooks are located cd ./rstudio/ && @@ -43,7 +38,7 @@ ]]> - + @@ -60,12 +55,12 @@ This familiar R analysis software suite will let you explore your datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr, LaTeX, bioconductor, cummeRbund, and many more pre-installed packages. - + Galaxy offers you to use RStudio directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in RStudio. - The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save(). + The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save(). - For example, gx_get(42) will fetch dataset 42 from your history and return the file location + For example, gx_get(42) will fetch dataset 42 from your history and return the file location From ae38c98f5adf246d4516ffe9248413099ef893aa Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 8 Oct 2019 14:52:54 +0200 Subject: [PATCH 09/86] add two more --- interactivetool_rstudio.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml index 9f39f227348..8338497f70c 100644 --- a/interactivetool_rstudio.xml +++ b/interactivetool_rstudio.xml @@ -13,6 +13,8 @@ ${__app__.config.galaxy_infrastructure_url} 8080 ${__app__.config.galaxy_infrastructure_url} + true + true #if $__user__: #for $api_key in $__user__.api_keys: From b92f4720273172cda4b64f96e0ce7e36e797893d Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 8 Oct 2019 14:53:31 +0200 Subject: [PATCH 10/86] also from prod --- interactivetool_jupyter_notebook.xml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml index 9dd3e36d3ee..60cdc00253f 100644 --- a/interactivetool_jupyter_notebook.xml +++ b/interactivetool_jupyter_notebook.xml @@ -39,7 +39,7 @@ ## copy default notebook cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb && jupyter trust ./ipython_galaxy_notebook.ipynb && - jupyter lab --no-browser --NotebookApp.shutdown_button=True && + jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True && cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook' #else: @@ -50,7 +50,7 @@ #if $mode.run_it: jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors ./*.ipynb && #else: - jupyter lab --no-browser --NotebookApp.shutdown_button=True && + jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True && #end if cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook' #end if @@ -88,13 +88,13 @@ The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. - + Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter. - + You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset. If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history. - + You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function. From 0bd3376068fe8d9059628b8ac127f4473d16eaf0 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 8 Oct 2019 14:59:38 +0200 Subject: [PATCH 11/86] switch version --- interactivetool_rstudio.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml index 8338497f70c..d0b11257a3f 100644 --- a/interactivetool_rstudio.xml +++ b/interactivetool_rstudio.xml @@ -1,6 +1,6 @@ - quay.io/erasche/docker-rstudio-notebook:19.05 + quay.io/erasche/docker-rstudio-notebook:19.09 From 8b5d5bf5c5812f101ae00a7e82b9f3c537ae32bf Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 8 Oct 2019 16:38:15 +0200 Subject: [PATCH 12/86] chown, hacks --- interactivetool_rstudio.xml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml index d0b11257a3f..8f5d8792bf4 100644 --- a/interactivetool_rstudio.xml +++ b/interactivetool_rstudio.xml @@ -35,7 +35,11 @@ sed -i 's|/monitor.*||g' /etc/services.d/nginx/run && - /init + ##/init + rstudio-server start && + /etc/init.d/syslog-ng start && + chmod 777 /tmp -R && + tail -f /var/log/rstudio-server/rserver.log ]]> From ca0624a341464c4c9b4d9409d509ce3b8cf64ea3 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 8 Oct 2019 16:48:42 +0200 Subject: [PATCH 13/86] fix pot --- interactivetool_rstudio.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml index 8f5d8792bf4..f15e9047cf4 100644 --- a/interactivetool_rstudio.xml +++ b/interactivetool_rstudio.xml @@ -4,7 +4,7 @@ - 80 + 8787 rstudio/ From 48b5cb7bc803031832114c49ab4f2c899fb11c2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 8 Oct 2019 20:09:27 +0200 Subject: [PATCH 14/86] latest RStudio changes --- interactivetool_rstudio.xml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml index f15e9047cf4..e6ee98af154 100644 --- a/interactivetool_rstudio.xml +++ b/interactivetool_rstudio.xml @@ -4,7 +4,7 @@ - 8787 + 80 rstudio/ @@ -35,9 +35,10 @@ sed -i 's|/monitor.*||g' /etc/services.d/nginx/run && - ##/init - rstudio-server start && /etc/init.d/syslog-ng start && + /init & + ##rstudio-server start && + sleep 5 && chmod 777 /tmp -R && tail -f /var/log/rstudio-server/rserver.log From d4403bc344cf2d4723bbdf9eefdef115141e56f0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 8 Oct 2019 20:09:53 +0200 Subject: [PATCH 15/86] use lab entrypoint --- interactivetool_jupyter_notebook.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml index 60cdc00253f..787d7fa64fa 100644 --- a/interactivetool_jupyter_notebook.xml +++ b/interactivetool_jupyter_notebook.xml @@ -5,7 +5,7 @@ 8888 - ipython/tree + ipython/lab From 4a558dba1ac0432b57b4bbd62b85adf8c5576a7d Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 8 Oct 2019 20:32:58 +0200 Subject: [PATCH 16/86] more reverts --- interactivetool_rstudio.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml index e6ee98af154..63e0eb3adb0 100644 --- a/interactivetool_rstudio.xml +++ b/interactivetool_rstudio.xml @@ -39,6 +39,7 @@ /init & ##rstudio-server start && sleep 5 && + chmod 777 /tmp -R && tail -f /var/log/rstudio-server/rserver.log From b050d84dbdeb31a95a35f0ab1ac84885daeb2718 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 9 Oct 2019 16:02:24 +0200 Subject: [PATCH 17/86] include env --- interactivetool_wilson.xml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml index 9d724a0fbe5..94abe38311d 100644 --- a/interactivetool_wilson.xml +++ b/interactivetool_wilson.xml @@ -8,10 +8,12 @@ 3838 + + feature_selection + &1 ]]> From 0dbfa7ce3282e003bc3158e622ee8e22815febe6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 9 Oct 2019 23:35:41 +0200 Subject: [PATCH 18/86] use own container --- interactivetool_wilson.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml index 94abe38311d..302ff3b0e4a 100644 --- a/interactivetool_wilson.xml +++ b/interactivetool_wilson.xml @@ -1,7 +1,7 @@ Webbased Interactive Omics visualization - loosolab/wilson:2.1.0 + quay.io/bgruening/wilson-app From 88e3f31dea523ed69ebfc4fe64a5075dc7096f48 Mon Sep 17 00:00:00 2001 From: root Date: Sat, 12 Oct 2019 00:37:59 +0200 Subject: [PATCH 19/86] fix phinch IE --- interactivetool_phinch.xml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/interactivetool_phinch.xml b/interactivetool_phinch.xml index d77c9274ad3..382cf32f0a9 100644 --- a/interactivetool_phinch.xml +++ b/interactivetool_phinch.xml @@ -1,4 +1,4 @@ - + shiltemann/docker-phinch-galaxy:16.04 @@ -11,12 +11,14 @@ ## ToDo nginx, proxy.conf etc can be removed from the container #import os - #set $name = os.path.splitext(str($infile.display_name))[0] + #set $name = os.path.splitext(str($infile.display_name).replace(' ', '_'))[0] ## in case someone names the data testdata. rm /home/Phinch/data/testdata.biom | true && - ln -s '$infile' /home/Phinch/data/${name}.biom && + ln -s '$infile' '/home/Phinch/data/${name}.biom' && cd /home/Phinch/data && sed -i "s/'REPLACE_ME'/'${name}.biom'/g" /home/Phinch/scripts/readFile.js && + sed -i "s/http/https/g" /home/Phinch/scripts/readFile.js && + ## keep it running cd /home/Phinch && php -S 0.0.0.0:80 2>&1 > /var/log/phinch.log From edd4da31e3a8077424cc3524bc4e988c74a17ddc Mon Sep 17 00:00:00 2001 From: root Date: Sat, 12 Oct 2019 12:16:45 +0200 Subject: [PATCH 20/86] Update Askomics. --- interactivetool_askomics.xml | 26 +++++++++++++++++++------- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml index c1ce9d3bd11..b4cb6bff0d1 100644 --- a/interactivetool_askomics.xml +++ b/interactivetool_askomics.xml @@ -1,17 +1,17 @@ - a visual SPARQL query builder + AskOmics, a visual SPARQL query builder - quay.io/askomics/askomics-ie:17.12_g19.09 + askomics/askomics-ie:19.01.3 6543 - /login_api_gie?key=abcd + /login_api_gie?key=${__user_name__} ${__app__.config.galaxy_infrastructure_url} - + #if $__user__: #for $api_key in $__user__.api_keys: ${api_key.key} @@ -19,15 +19,26 @@ #end for #end if + ${__user_name__} + ${__user_email__} + ${__user_name__} + From 30424102deb606e69b8e29505d722bdee298d821 Mon Sep 17 00:00:00 2001 From: root Date: Sat, 12 Oct 2019 16:35:42 +0200 Subject: [PATCH 21/86] make bam.io.bio work --- interactivetool_bam_iobio.xml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/interactivetool_bam_iobio.xml b/interactivetool_bam_iobio.xml index 2f1c531861c..6c78eaa335b 100644 --- a/interactivetool_bam_iobio.xml +++ b/interactivetool_bam_iobio.xml @@ -21,6 +21,9 @@ sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" js/bam.iobio.js/bam.iobio.js && sed -i "s@\"wss://services.iobio.io/samheader/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samheader/\"@" js/bam.iobio.js/bam.iobio.js && + + sed -i 's/deny all;//g' /etc/nginx/nginx.conf && + cp '${infile}' /input/bamfile.bam && cp '${infile.metadata.bam_index}' /input/bamfile.bam.bai && mkdir /var/log/supervisor/ && From fec1801d07540dccb0af8d20c71833f659b97961 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jens=20Preu=C3=9Fner?= Date: Mon, 14 Oct 2019 14:43:40 +0200 Subject: [PATCH 22/86] Handle env vars; updated container to latest tag --- interactivetool_wilson.xml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml index 302ff3b0e4a..c362a758c4e 100644 --- a/interactivetool_wilson.xml +++ b/interactivetool_wilson.xml @@ -1,7 +1,7 @@ Webbased Interactive Omics visualization - quay.io/bgruening/wilson-app + loosolab/wilson:2.1.1 @@ -10,9 +10,12 @@ feature_selection + true /home/shiny/.Renviron && + echo $WILSON_BLACKLIST_EXAMPLES >> /home/shiny/.Renviron && ln -s ${infile} /srv/shiny-server/external_data/input.clarion && exec shiny-server 2>&1 ]]> From a4f9346b67fbf35fef2c8211d323a5bfb5ba3d3a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jens=20Preu=C3=9Fner?= Date: Wed, 16 Oct 2019 09:39:31 +0200 Subject: [PATCH 23/86] Fixed bug in command for .Renviron construction --- interactivetool_wilson.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml index c362a758c4e..7f575c43a63 100644 --- a/interactivetool_wilson.xml +++ b/interactivetool_wilson.xml @@ -14,8 +14,8 @@ /home/shiny/.Renviron && - echo $WILSON_BLACKLIST_EXAMPLES >> /home/shiny/.Renviron && + echo "WILSON_LANDING_PAGE=\$WILSON_LANDING_PAGE" > /home/shiny/.Renviron && + echo "WILSON_BLACKLIST_EXAMPLES=\$WILSON_BLACKLIST_EXAMPLES" >> /home/shiny/.Renviron && ln -s ${infile} /srv/shiny-server/external_data/input.clarion && exec shiny-server 2>&1 ]]> From c136c13c5b4bc947ff9dad803c1fd60d818f958f Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 16 Oct 2019 14:26:04 +0200 Subject: [PATCH 24/86] add wallace IT --- interactivetool_wallace.xml | 53 +++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 interactivetool_wallace.xml diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml new file mode 100644 index 00000000000..83d70d19f0c --- /dev/null +++ b/interactivetool_wallace.xml @@ -0,0 +1,53 @@ + + Webbased Interactive modeling of species niches and distributions + + quay.io/bgruening/wilson-app + + + + 3838 + /sample-apps/SIG/wallace/shiny/ + + + + ${__app__.security.encode_id($jupyter_notebook.history_id)} + ${__app__.config.galaxy_infrastructure_url} + 8080 + ${__app__.config.galaxy_infrastructure_url} + + #if $__user__: + #for $api_key in $__user__.api_keys: + ${api_key.key} + #break + #end for + #end if + + + + + + + + + + + + + +`_ is a modular platform for reproducible modeling of species niches and distributions. + +.. class:: infomark + + + +]]> + + + 10.1111/2041-210X.12945 + + From fae69abcf39a1833dfda755114627c35b2d6dffa Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 16 Oct 2019 14:39:58 +0200 Subject: [PATCH 25/86] some updates --- interactivetool_wallace.xml | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml index 83d70d19f0c..6a36204caaf 100644 --- a/interactivetool_wallace.xml +++ b/interactivetool_wallace.xml @@ -1,7 +1,7 @@ Webbased Interactive modeling of species niches and distributions - quay.io/bgruening/wilson-app + ylebras/wallace-docker @@ -32,18 +32,30 @@ - + `_ is a modular platform for reproducible modeling of species niches and distributions. .. class:: infomark +Example input file (TAB separated):: + "name" "longitude" "latitude" "countryCode" + Accipiter striatus Vieillot, 1808 -60.291838 46.328137 CA + Accipiter striatus Vieillot, 1808 -114.58927 35.022485 US + Accipiter striatus Vieillot, 1808 -93.37406 30.00586 US + Accipiter striatus Vieillot, 1808 -79.336288 43.682218 CA + Accipiter striatus Vieillot, 1808 -109.156024 31.904185 US + Accipiter striatus Vieillot, 1808 -71.098031 42.297408 US + Accipiter striatus Vieillot, 1808 -110.927215 32.18203 US ]]> From 0d6bc47d2ea2b55eab60f8487978e55635e4f85e Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Wed, 16 Oct 2019 16:34:10 +0200 Subject: [PATCH 26/86] Update interactivetool_wallace.xml --- interactivetool_wallace.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml index 6a36204caaf..66001ee97b9 100644 --- a/interactivetool_wallace.xml +++ b/interactivetool_wallace.xml @@ -29,10 +29,10 @@ ]]> - + - + @@ -42,7 +42,7 @@ -`Wallace `_ is a modular platform for reproducible modeling of species niches and distributions. +`Wallace `_ is a flexible platform for reproducible modeling of species niches and distributions. .. class:: infomark From b6f4fbb1a54657b6d5be4d350f7364652a992c1b Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Wed, 16 Oct 2019 17:05:44 +0200 Subject: [PATCH 27/86] update container input dataset folder After verification --- interactivetool_wallace.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml index 66001ee97b9..5dbf29dfd30 100644 --- a/interactivetool_wallace.xml +++ b/interactivetool_wallace.xml @@ -24,7 +24,7 @@ From b831ce30d1753081d0f95b1bea86cabaa6a86038 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Wed, 16 Oct 2019 17:35:00 +0200 Subject: [PATCH 28/86] only consider csv occurence file as input for now --- interactivetool_wallace.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml index 5dbf29dfd30..b860dd01267 100644 --- a/interactivetool_wallace.xml +++ b/interactivetool_wallace.xml @@ -29,10 +29,10 @@ ]]> - + - + From f91eb0679ffb88bbe448daa6de4ee5c6c63b2a92 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Wed, 16 Oct 2019 17:46:12 +0200 Subject: [PATCH 29/86] As we will use Galaxy_helper no need to import data on the fly --- interactivetool_wallace.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml index b860dd01267..cd958ee3d6c 100644 --- a/interactivetool_wallace.xml +++ b/interactivetool_wallace.xml @@ -24,7 +24,6 @@ From 7a75856cd19c83ef5eecf15fce9f7f3af0e5d40c Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Wed, 16 Oct 2019 17:57:14 +0200 Subject: [PATCH 30/86] comment input and output --- interactivetool_wallace.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml index cd958ee3d6c..14b03ac3d3d 100644 --- a/interactivetool_wallace.xml +++ b/interactivetool_wallace.xml @@ -28,10 +28,10 @@ ]]> - + - + From 7bdf4c9c0901924d30effc784c53aa748dd5b78a Mon Sep 17 00:00:00 2001 From: root Date: Wed, 16 Oct 2019 19:29:53 +0200 Subject: [PATCH 31/86] wallace changes --- interactivetool_wallace.xml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml index 14b03ac3d3d..4d8e2c5353b 100644 --- a/interactivetool_wallace.xml +++ b/interactivetool_wallace.xml @@ -4,13 +4,14 @@ ylebras/wallace-docker - + 3838 /sample-apps/SIG/wallace/shiny/ - ${__app__.security.encode_id($jupyter_notebook.history_id)} + + ${__app__.security.encode_id($outfile.history_id)} ${__app__.config.galaxy_infrastructure_url} 8080 ${__app__.config.galaxy_infrastructure_url} @@ -24,14 +25,16 @@ - + From 4599cabec1100eab48286e6caa66d065061d9572 Mon Sep 17 00:00:00 2001 From: root Date: Wed, 23 Oct 2019 19:43:04 +0200 Subject: [PATCH 32/86] update askomics to version 1.0 --- interactivetool_askomics.xml | 56 ++++++++++++++++++++---------------- 1 file changed, 32 insertions(+), 24 deletions(-) diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml index b4cb6bff0d1..2dd06fe28ba 100644 --- a/interactivetool_askomics.xml +++ b/interactivetool_askomics.xml @@ -1,16 +1,25 @@ - - AskOmics, a visual SPARQL query builder + + a visual SPARQL query builder - askomics/askomics-ie:19.01.3 + askomics/flaskomics-with-dependencies:3.1.1 - 6543 - /login_api_gie?key=${__user_name__} + 5000 + /loginapikey/${__user_name__} + + true + ${__user_name__} + Galaxy + ${__user_name__} + ${__user_email__} + ${__user_name__} + ${__app__.config.galaxy_infrastructure_url} + #if $__user__: #for $api_key in $__user__.api_keys: @@ -19,27 +28,26 @@ #end for #end if - ${__user_name__} - ${__user_email__} - ${__user_name__} + + prod + 1 + Galaxy + AskOmics Interactive Tool for Galaxy + /tmp/askomics-it + /tmp/askomics-it/database.db + http://localhost:5000 + + true + + 85000 + 65000 - + From 8bbc6f69feda269e8b04208cf9577c4381721954 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Thu, 24 Oct 2019 17:12:21 -0400 Subject: [PATCH 33/86] Galaxy InteractiveTools cluster fixes from EU --- interactivetool_jupyter_notebook.xml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml index 9dd3e36d3ee..60cdc00253f 100644 --- a/interactivetool_jupyter_notebook.xml +++ b/interactivetool_jupyter_notebook.xml @@ -39,7 +39,7 @@ ## copy default notebook cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb && jupyter trust ./ipython_galaxy_notebook.ipynb && - jupyter lab --no-browser --NotebookApp.shutdown_button=True && + jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True && cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook' #else: @@ -50,7 +50,7 @@ #if $mode.run_it: jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors ./*.ipynb && #else: - jupyter lab --no-browser --NotebookApp.shutdown_button=True && + jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True && #end if cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook' #end if @@ -88,13 +88,13 @@ The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. - + Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter. - + You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset. If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history. - + You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function. From a408f3e479f4a17cf53756ddf106fbde009791ad Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 28 Oct 2019 15:58:40 -0400 Subject: [PATCH 34/86] Structured access to Galaxy internals for ITs. --- interactivetool_askomics.xml | 11 ++--------- interactivetool_jupyter_notebook.xml | 15 ++++----------- 2 files changed, 6 insertions(+), 20 deletions(-) diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml index c1ce9d3bd11..7f997b54e63 100644 --- a/interactivetool_askomics.xml +++ b/interactivetool_askomics.xml @@ -10,15 +10,8 @@ - ${__app__.config.galaxy_infrastructure_url} - - #if $__user__: - #for $api_key in $__user__.api_keys: - ${api_key.key} - #break - #end for - #end if - + $__galaxy_url + - ${__app__.security.encode_id($jupyter_notebook.history_id)} - ${__app__.config.galaxy_infrastructure_url} + $__history_id + $__galaxy_url 8080 - ${__app__.config.galaxy_infrastructure_url} - - #if $__user__: - #for $api_key in $__user__.api_keys: - ${api_key.key} - #break - #end for - #end if - + $__galaxy_url + Date: Tue, 29 Oct 2019 08:29:02 -0400 Subject: [PATCH 35/86] Cleanup structured IT internals access commit. - Unit test fixes and added tests. - Change __history_id to __history_id__ per comment from @bgruening --- interactivetool_askomics.xml | 2 +- interactivetool_jupyter_notebook.xml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml index 7f997b54e63..b5f0b4d56a4 100644 --- a/interactivetool_askomics.xml +++ b/interactivetool_askomics.xml @@ -10,7 +10,7 @@ - $__galaxy_url + $__galaxy_url__ - $__history_id - $__galaxy_url + $__history_id__ + $__galaxy_url__ 8080 - $__galaxy_url + $__galaxy_url__ Date: Tue, 12 Nov 2019 00:59:32 +0100 Subject: [PATCH 36/86] add pyiron tool --- interactivetool_pyiron.xml | 96 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 interactivetool_pyiron.xml diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml new file mode 100644 index 00000000000..d56abbb3b66 --- /dev/null +++ b/interactivetool_pyiron.xml @@ -0,0 +1,96 @@ + + + quay.io/bgruening/docker-jupyter-notebook:pyiron + + + + 8888 + ipython/lab + + + + $__history_id__ + $__galaxy_url__ + 8080 + $__galaxy_url__ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pyiron - an integrated development environment (IDE) for computational materials science. It combines several tools in a common platform: + + The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, + visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, + machine learning, and much more. + + Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to + do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter. + + You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset. + If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history. + + You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function. + + From 9eabec14dffb25a8a69bf8d186d26f710fd7db76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 12 Nov 2019 09:37:05 +0100 Subject: [PATCH 37/86] add new envs to pyiron --- interactivetool_pyiron.xml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml index d56abbb3b66..0f5ac65a00f 100644 --- a/interactivetool_pyiron.xml +++ b/interactivetool_pyiron.xml @@ -14,10 +14,13 @@ 8080 $__galaxy_url__ + /home/jovyan/resources Date: Tue, 12 Nov 2019 10:48:13 +0100 Subject: [PATCH 38/86] small edits to pyiron --- interactivetool_pyiron.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml index 0f5ac65a00f..9657bc87c3b 100644 --- a/interactivetool_pyiron.xml +++ b/interactivetool_pyiron.xml @@ -3,7 +3,7 @@ quay.io/bgruening/docker-jupyter-notebook:pyiron - + 8888 ipython/lab @@ -70,7 +70,7 @@ - + From 8c752d470358d1fc561764299aa7a40092ba2ca9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 12 Nov 2019 10:55:57 +0100 Subject: [PATCH 39/86] use proper PWD --- interactivetool_pyiron.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml index 9657bc87c3b..68d59040727 100644 --- a/interactivetool_pyiron.xml +++ b/interactivetool_pyiron.xml @@ -18,8 +18,8 @@ Date: Tue, 12 Nov 2019 13:54:09 +0100 Subject: [PATCH 40/86] Update interactivetool_pyiron.xml --- interactivetool_pyiron.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/interactivetool_pyiron.xml b/interactivetool_pyiron.xml index 68d59040727..69caecdf71b 100644 --- a/interactivetool_pyiron.xml +++ b/interactivetool_pyiron.xml @@ -29,6 +29,7 @@ ## change into the directory where the notebooks are located cd ./jupyter/ && + cp \${HOME}/examples/* ./ && export PATH=/home/jovyan/.local/bin:\$PATH && #if $mode.mode_select == 'scratch': From f953b39beacb6f628a08a6c5fba236891e0c214f Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 13 Nov 2019 16:29:48 +0100 Subject: [PATCH 41/86] add guacamole_desktop --- interactivetool_guacamole_desktop.xml | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 interactivetool_guacamole_desktop.xml diff --git a/interactivetool_guacamole_desktop.xml b/interactivetool_guacamole_desktop.xml new file mode 100644 index 00000000000..a63ce108991 --- /dev/null +++ b/interactivetool_guacamole_desktop.xml @@ -0,0 +1,26 @@ + + + cyverse/ubuntu18-xfce-desktop + + + + 8000 + + + + + + + + + + + + + Simple Ubuntu XFCE all-in-one desktop. + Username: "user" + Password: "password" + + From 99da6e95b01f1051f5393bbb14fc5bb383183a8f Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 14 Nov 2019 02:16:18 +0100 Subject: [PATCH 42/86] several enhancements and fixes --- interactivetool_guacamole_desktop.xml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/interactivetool_guacamole_desktop.xml b/interactivetool_guacamole_desktop.xml index a63ce108991..665f4d33eb8 100644 --- a/interactivetool_guacamole_desktop.xml +++ b/interactivetool_guacamole_desktop.xml @@ -1,13 +1,15 @@ - cyverse/ubuntu18-xfce-desktop + quay.io/bgruening/guacamole-desktop - 8000 + 8080 + - @@ -19,8 +21,7 @@ - Simple Ubuntu XFCE all-in-one desktop. - Username: "user" - Password: "password" + Simple Ubuntu XFCE all-in-one desktop. The Username is "user" and the Password is "password". + This image is based on the awesome work from CyVerse. From ce872ac1ae789a8770ddf037fc75170a73e35816 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 25 Nov 2019 22:16:04 +0100 Subject: [PATCH 43/86] add new interactive VCF tool --- interactivetool_vcf_iobio.xml | 54 +++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 interactivetool_vcf_iobio.xml diff --git a/interactivetool_vcf_iobio.xml b/interactivetool_vcf_iobio.xml new file mode 100644 index 00000000000..898a34f7444 --- /dev/null +++ b/interactivetool_vcf_iobio.xml @@ -0,0 +1,54 @@ + + + qiaoy/iobio-bundle.vcf-iobio:dev-ondemand + + + + 80 + + + + /tmp/app.conf && + mv /tmp/app.conf /etc/supervisor.d/app.conf && + + /usr/bin/supervisord -c /etc/supervisord.conf + ]]> + + + + + + + + + + + VCF iobio visualisation. + + From 5ff93313a59871f6cb620924403caae8e6e0afba Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 26 Nov 2019 09:27:22 +0100 Subject: [PATCH 44/86] add climate notebook --- interactivetool_climate_notebook.xml | 95 ++++++++++++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 interactivetool_climate_notebook.xml diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml new file mode 100644 index 00000000000..1d12e46316e --- /dev/null +++ b/interactivetool_climate_notebook.xml @@ -0,0 +1,95 @@ + + + nordicesmhub/docker-climate-notebook:1.0 + + + + 8888 + ipython/lab + + + + $__history_id__ + $__galaxy_url__ + 8080 + $__galaxy_url__ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The Climate Notebook is based on Jupyter an open-source web application that allows you to create and share documents that contain live code, equations, + visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, + machine learning, and much more. + + Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to + do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter. + + You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset. + If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history. + + You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function. + + The Climate version of the Jupyter Notebook offers a lot of preinstalled tools for climate science. + + From 03dc5828f9a402ce23675a9de841d921b147afe5 Mon Sep 17 00:00:00 2001 From: Anne Fouilloux Date: Tue, 26 Nov 2019 13:30:13 +0100 Subject: [PATCH 45/86] complement help for interactive climate notebook by adding the list of available packages and a link to pangeo --- interactivetool_climate_notebook.xml | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml index 1d12e46316e..aa1692ada80 100644 --- a/interactivetool_climate_notebook.xml +++ b/interactivetool_climate_notebook.xml @@ -90,6 +90,22 @@ You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function. - The Climate version of the Jupyter Notebook offers a lot of preinstalled tools for climate science. + The Climate version of the Jupyter Notebook offers a lot of preinstalled tools for climate science. The list of packages is based on what is available + on the [Pangeo](http://pangeo.io/) platform and [Pangeo stacks](https://pangeo-data.github.io/pangeo-stacks/). + + - **Core scipy packages**: numpy, scipy, matplotlib, pandas, xarray, sparse and sympy + - **Data science**: scikit-image, scikit-learn, dask-ml, tensorflow, keras, pytorch-cpu, dask_labextension + - **Visualization**: holoviews, panel, geoviews, hvplot, geoviews, datashader, seaborn, altair, descartes, folium, vega, + vega_datasets, palettable, cmocean,plotly, psy-maps, psy-reg, psyplot, psyplot-gui, psy-maps, psy-reg, + geopy, branca + - **Geospatial**: iris, cartopy, basemap, basemap-data-hires, geopandas, rasterio, netcdf4, erddapy, pydap, h5py, h5netcdf, regionmask and rio-cogeo + - **Geoscience related**: climlab, metpy, satpy, gsw, eofs, esmpy, xesmf, windspharm, rasterstats, geojsoncontour + - **Climate related**: pyaerocom, cdo, cdsapi, cfgrib, cis. esmvaltool, nc-time-axis, nco + - **Intake related**: intake, intake-xarray, intake-esm, fsspec and intake-stac + - **zarr related**: zarr, numcodecs, python-blosc, lz4, gcsfs, s3fs, tiledb-py + - **jupyter related**: ipyleaflet, papermill, jupytext, ipydatawidgets, sidecar + - **xarray related**: xgcm, xrft, xhistogram, xlrd, xrviz, climpred, pytide, pyinterp + - **misc**: python-wget, prefect, requests, pillow, pip, nbgitpuller, pysplit, biopython, bioblend and galaxy-ie-helpers + From 91d2eea4ae54ef5f3f03000757dddef135d76290 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 26 Nov 2019 17:13:14 +0100 Subject: [PATCH 46/86] add some VCF fixes --- interactivetool_vcf_iobio.xml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/interactivetool_vcf_iobio.xml b/interactivetool_vcf_iobio.xml index 898a34f7444..4bb1d4eeec9 100644 --- a/interactivetool_vcf_iobio.xml +++ b/interactivetool_vcf_iobio.xml @@ -16,12 +16,12 @@ #set $PUB_HTTP_PORT = '80' cd /var/www/html && - ##sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" js/bam.iobio.js/bam.iobio.js && - ##sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" js/bam.iobio.js/bam.iobio.js && - sed -i "s@\"wss://services.iobio.io/vcfreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfreaddepther/\"@" js/vcf.iobio.js/vcf.iobio.js && - sed -i "s@\"wss://services.iobio.io/vcfstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfstatsalive/\"@" js/vcf.iobio.js/vcf.iobio.js && - ##sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" js/bam.iobio.js/bam.iobio.js && - sed -i "s@\"wss://services.iobio.io/tabix/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/tabix/\"@" js/vcf.iobio.js/vcf.iobio.js && + ##sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" app/bam.iobio.js && + ##sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" app/bam.iobio.js && + sed -i "s@\"wss://services.iobio.io/vcfdepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfdepther/\"@" app/vcf.iobio.js && + sed -i "s@\"wss://services.iobio.io/vcfstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfstatsalive/\"@" app/vcf.iobio.js && + ##sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" app/bam.iobio.js && + sed -i "s@\"wss://services.iobio.io/tabix/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/tabix/\"@" app/vcf.iobio.js && ##s@ws://tabix.iobio.io@ws://" + window.location.hostname + ":8000@ From da4d1a043c47f38c4228e397b9847c55c62fb20c Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Tue, 26 Nov 2019 19:58:33 +0100 Subject: [PATCH 47/86] update vcf IE --- interactivetool_vcf_iobio.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/interactivetool_vcf_iobio.xml b/interactivetool_vcf_iobio.xml index 4bb1d4eeec9..dc585d8818c 100644 --- a/interactivetool_vcf_iobio.xml +++ b/interactivetool_vcf_iobio.xml @@ -5,7 +5,7 @@ 80 - + /tmp/app.conf && mv /tmp/app.conf /etc/supervisor.d/app.conf && From eb84e6743d81ad1fc602085f5c10b8500ad82486 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Wed, 27 Nov 2019 13:14:19 +0100 Subject: [PATCH 48/86] add latest VCF changes --- interactivetool_vcf_iobio.xml | 39 ++++++++++++++++------------------- 1 file changed, 18 insertions(+), 21 deletions(-) diff --git a/interactivetool_vcf_iobio.xml b/interactivetool_vcf_iobio.xml index dc585d8818c..3be0266c593 100644 --- a/interactivetool_vcf_iobio.xml +++ b/interactivetool_vcf_iobio.xml @@ -5,49 +5,46 @@ 80 - + /tmp/app.conf && + mv /tmp/app.conf /etc/supervisor.d/app.conf && + /usr/bin/supervisord -c /etc/supervisord.conf - sed -i 's/deny all;//g' /etc/nginx/nginx.conf && - - cp '${infile}' /input/vcffile.vcf && - ##cp '${infile.metadata.bam_index}' /input/vcffile.bam.bai && - head -n -2 /etc/supervisor.d/app.conf > /tmp/app.conf && - mv /tmp/app.conf /etc/supervisor.d/app.conf && - - /usr/bin/supervisord -c /etc/supervisord.conf ]]> - + - - VCF iobio visualisation. + `_. + +This visualization is using Galaxy Interactive Tool and utilizes an all-in-one Docker container from http://iobio.io. + +Make sure your VCF file is compressed to the vcf_bgzip datatype to load it into the Visualization. + ]]> + From a6ed2d61ba622850748963327b6f63c4ffbfa72a Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Sat, 30 Nov 2019 22:46:10 +0100 Subject: [PATCH 49/86] A first try of openrefine GIE -> interactivetool --- interactivetool_openrefine.xml | 64 ++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 interactivetool_openrefine.xml diff --git a/interactivetool_openrefine.xml b/interactivetool_openrefine.xml new file mode 100644 index 00000000000..17680fb6d0e --- /dev/null +++ b/interactivetool_openrefine.xml @@ -0,0 +1,64 @@ + + Working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data. + + ylebras/openrefine-docker + + + + 80 + + + + + + ${__app__.security.encode_id($outfile.history_id)} + ${__app__.config.galaxy_infrastructure_url} + 8080 + ${__app__.config.galaxy_infrastructure_url} + + #if $__user__: + #for $api_key in $__user__.api_keys: + ${api_key.key} + #break + #end for + #end if + + + + + + + + + + + + + +`_ (previously Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data. + +.. class:: infomark + +Example input file (TAB separated):: + + "name" "longitude" "latitude" "countryCode" + Accipiter striatus Vieillot, 1808 -60.291838 46.328137 CA + Accipiter striatus Vieillot, 1808 -114.58927 35.022485 US + Accipiter striatus Vieillot, 1808 -93.37406 30.00586 US + Accipiter striatus Vieillot, 1808 -79.336288 43.682218 CA + Accipiter striatus Vieillot, 1808 -109.156024 31.904185 US + Accipiter striatus Vieillot, 1808 -71.098031 42.297408 US + Accipiter striatus Vieillot, 1808 -110.927215 32.18203 US + +]]> + + From a97099d7cced23d10f4833a2c2f9ff7ce331924f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sun, 1 Dec 2019 14:17:01 +0100 Subject: [PATCH 50/86] so this should work, I hope --- interactivetool_openrefine.xml | 63 ++++++++++++++++++++-------------- 1 file changed, 38 insertions(+), 25 deletions(-) diff --git a/interactivetool_openrefine.xml b/interactivetool_openrefine.xml index 17680fb6d0e..956073db48a 100644 --- a/interactivetool_openrefine.xml +++ b/interactivetool_openrefine.xml @@ -1,32 +1,46 @@ - - Working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data. + + Working with messy data ylebras/openrefine-docker - 80 - + 3333 - - ${__app__.security.encode_id($outfile.history_id)} - ${__app__.config.galaxy_infrastructure_url} + $__history_id__ + $__galaxy_url__ 8080 - ${__app__.config.galaxy_infrastructure_url} - - #if $__user__: - #for $api_key in $__user__.api_keys: - ${api_key.key} - #break - #end for - #end if - + $__galaxy_url__ + - + \&1) +while [[ \${STATUS} =~ "refused" ]] +do + echo "Waiting for openrefine: \$STATUS \n" + STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>\&1) + sleep 4 +done +]]> + + + @@ -34,17 +48,16 @@ - + + + - -`_ (previously Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data. +`Openrefine `_ (previously Google Refine) is a powerful tool for working with messy data: +cleaning it; transforming it from one format into another; and extending it with web services and external data. .. class:: infomark From 466d8d38ab48a829205e17a37d38f581aa90db6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sun, 1 Dec 2019 14:34:43 +0100 Subject: [PATCH 51/86] small fix --- interactivetool_openrefine.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/interactivetool_openrefine.xml b/interactivetool_openrefine.xml index 956073db48a..11a0b01ffc3 100644 --- a/interactivetool_openrefine.xml +++ b/interactivetool_openrefine.xml @@ -20,11 +20,11 @@ exec /OpenRefine/refine -i 0.0.0.0 -m \$GALAXY_MEMORY_MB & ##Check if openrefine is up to work -STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>\&1) +STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>&1) while [[ \${STATUS} =~ "refused" ]] do echo "Waiting for openrefine: \$STATUS \n" - STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>\&1) + STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>&1) sleep 4 done ]]> From 7fcbf9c6dd142d91c6f5cabd6d067f3be4e81c76 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Mon, 2 Dec 2019 11:34:43 +0100 Subject: [PATCH 52/86] Create interactivetool_radiant.xml First try --- interactivetool_radiant.xml | 75 +++++++++++++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 interactivetool_radiant.xml diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml new file mode 100644 index 00000000000..d48cd9cf126 --- /dev/null +++ b/interactivetool_radiant.xml @@ -0,0 +1,75 @@ + + Data analytics using Radiant R Shiny app + + ylebras/radiant-docker + + + + 3838 + /sample-apps/STAT/ + + + + + ${__app__.security.encode_id($outfile.history_id)} + ${__app__.config.galaxy_infrastructure_url} + 8080 + ${__app__.config.galaxy_infrastructure_url} + + #if $__user__: + #for $api_key in $__user__.api_keys: + ${api_key.key} + #break + #end for + #end if + + + + + + + + + + + + + +`_ is an open-source platform-independent browser-based interface for business analytics in R. The application is based on the Shiny package and can be run locally or on a server. Radiant was developed by Vincent Nijs. Please use the issue tracker on GitHub to suggest enhancements or report problems: https://github.com/radiant-rstats/radiant/issues. For other questions and comments please use radiant@rady.ucsd.edu. +Key features + +- Explore: Quickly and easily summarize, visualize, and analyze your data +- Cross-platform: It runs in a browser on Windows, Mac, and Linux +- Reproducible: Recreate results and share work with others as a state file or an Rmarkdown report +- Programming: Integrate Radiant’s analysis functions with your own R-code +- Context: Data and examples focus on business applications + + +.. class:: infomark + +Example input file (TAB separated):: + + "name" "longitude" "latitude" "countryCode" + Accipiter striatus Vieillot, 1808 -60.291838 46.328137 CA + Accipiter striatus Vieillot, 1808 -114.58927 35.022485 US + Accipiter striatus Vieillot, 1808 -93.37406 30.00586 US + Accipiter striatus Vieillot, 1808 -79.336288 43.682218 CA + Accipiter striatus Vieillot, 1808 -109.156024 31.904185 US + Accipiter striatus Vieillot, 1808 -71.098031 42.297408 US + Accipiter striatus Vieillot, 1808 -110.927215 32.18203 US + +]]> + + + + + From b9df1d6eb01024381abbf0d5f7b87646829e1bca Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Mon, 2 Dec 2019 11:47:00 +0100 Subject: [PATCH 53/86] Create interactivetool_geoexplorer.xml --- interactivetool_geoexplorer.xml | 69 +++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 interactivetool_geoexplorer.xml diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml new file mode 100644 index 00000000000..ba51c7c70ed --- /dev/null +++ b/interactivetool_geoexplorer.xml @@ -0,0 +1,69 @@ + + An interactive spatial analysis platform using ggvis and Leaflet + + ylebras/geoexplorer-docker + + + + 3838 + /sample-apps/SIG/ + + + + + ${__app__.security.encode_id($outfile.history_id)} + ${__app__.config.galaxy_infrastructure_url} + 8080 + ${__app__.config.galaxy_infrastructure_url} + + #if $__user__: + #for $api_key in $__user__.api_keys: + ${api_key.key} + #break + #end for + #end if + + + + + + + + + + + + + +`_ is An interactive spatial analysis platform using ggvis and Leaflet. + +Author: David Stephens + +App: http://www.davesteps.com/geoExploreR/ + +.. class:: infomark + +Example input file (TAB separated):: + + "name" "longitude" "latitude" "countryCode" + Accipiter striatus Vieillot, 1808 -60.291838 46.328137 CA + Accipiter striatus Vieillot, 1808 -114.58927 35.022485 US + Accipiter striatus Vieillot, 1808 -93.37406 30.00586 US + Accipiter striatus Vieillot, 1808 -79.336288 43.682218 CA + Accipiter striatus Vieillot, 1808 -109.156024 31.904185 US + Accipiter striatus Vieillot, 1808 -71.098031 42.297408 US + Accipiter striatus Vieillot, 1808 -110.927215 32.18203 US + +]]> + + + + + From ea43b3c5b5a5b62a12b820d50712a93006231df5 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Mon, 2 Dec 2019 13:56:23 +0100 Subject: [PATCH 54/86] correct Galaxy environment variables --- interactivetool_geoexplorer.xml | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml index ba51c7c70ed..0667c42d5d7 100644 --- a/interactivetool_geoexplorer.xml +++ b/interactivetool_geoexplorer.xml @@ -10,19 +10,12 @@ - - ${__app__.security.encode_id($outfile.history_id)} - ${__app__.config.galaxy_infrastructure_url} + $__history_id__ + $__galaxy_url__ 8080 - ${__app__.config.galaxy_infrastructure_url} - - #if $__user__: - #for $api_key in $__user__.api_keys: - ${api_key.key} - #break - #end for - #end if - + $__galaxy_url__ + + Date: Mon, 2 Dec 2019 13:57:32 +0100 Subject: [PATCH 55/86] correct env variables --- interactivetool_radiant.xml | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml index d48cd9cf126..7b87bfe3ead 100644 --- a/interactivetool_radiant.xml +++ b/interactivetool_radiant.xml @@ -10,19 +10,12 @@ - - ${__app__.security.encode_id($outfile.history_id)} - ${__app__.config.galaxy_infrastructure_url} + $__history_id__ + $__galaxy_url__ 8080 - ${__app__.config.galaxy_infrastructure_url} - - #if $__user__: - #for $api_key in $__user__.api_keys: - ${api_key.key} - #break - #end for - #end if - + $__galaxy_url__ + + Date: Mon, 2 Dec 2019 14:10:39 +0100 Subject: [PATCH 56/86] update citation --- interactivetool_geoexplorer.xml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml index 0667c42d5d7..894dd590c23 100644 --- a/interactivetool_geoexplorer.xml +++ b/interactivetool_geoexplorer.xml @@ -57,6 +57,12 @@ Example input file (TAB separated):: ]]> - + @misc{githubsurvey2018, + author = {davesteps}, + title = {{dashboard to visualise geographic data}}, + publisher = {Github}, + url = {https://github.com/davesteps/geoExploreR} + } + } From 980b7344a1d3019e22ff64b438383da654dab4fd Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Mon, 2 Dec 2019 14:12:40 +0100 Subject: [PATCH 57/86] update citation --- interactivetool_radiant.xml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml index 7b87bfe3ead..ef7165b9897 100644 --- a/interactivetool_radiant.xml +++ b/interactivetool_radiant.xml @@ -63,6 +63,12 @@ Example input file (TAB separated):: ]]> - + @misc{githubsurvey2018, + author = {vnijs}, + title = {{Radiant - Business analytics using R and Shiny}}, + publisher = {Github}, + url = {https://github.com/vnijs/radiant} + } + } From c4b5f3ff41e958b3f06897dd4e4c22897b8b7d6a Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Mon, 2 Dec 2019 14:15:14 +0100 Subject: [PATCH 58/86] remove empty lines --- interactivetool_radiant.xml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml index ef7165b9897..40615e71a0a 100644 --- a/interactivetool_radiant.xml +++ b/interactivetool_radiant.xml @@ -18,9 +18,7 @@ @@ -33,10 +31,6 @@ `_ is an open-source platform-independent browser-based interface for business analytics in R. The application is based on the Shiny package and can be run locally or on a server. Radiant was developed by Vincent Nijs. Please use the issue tracker on GitHub to suggest enhancements or report problems: https://github.com/radiant-rstats/radiant/issues. For other questions and comments please use radiant@rady.ucsd.edu. Key features @@ -46,7 +40,6 @@ Key features - Programming: Integrate Radiant’s analysis functions with your own R-code - Context: Data and examples focus on business applications - .. class:: infomark Example input file (TAB separated):: From b4bc34122677563dcd6f8c328b584fef3890ec27 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Mon, 2 Dec 2019 17:30:55 +0100 Subject: [PATCH 59/86] modify url --- interactivetool_radiant.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml index 40615e71a0a..691a6ec1ae9 100644 --- a/interactivetool_radiant.xml +++ b/interactivetool_radiant.xml @@ -6,7 +6,7 @@ 3838 - /sample-apps/STAT/ + /sample-apps/STAT/inst/app From b5bcaead979c8cc04d24bb77a95cc30c1bb19597 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 2 Dec 2019 20:15:58 +0100 Subject: [PATCH 60/86] small changes to new ITs --- interactivetool_geoexplorer.xml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml index 894dd590c23..d709f0c0360 100644 --- a/interactivetool_geoexplorer.xml +++ b/interactivetool_geoexplorer.xml @@ -15,19 +15,23 @@ 8080 $__galaxy_url__ - > /var/log/shiny-server.log 2>&1 ]]> - + - + From 53bc67882fef3797bfacc9608d6a953098fe98ad Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 2 Dec 2019 20:16:03 +0100 Subject: [PATCH 61/86] small changes to new ITs --- interactivetool_radiant.xml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml index 40615e71a0a..ba84b9f4372 100644 --- a/interactivetool_radiant.xml +++ b/interactivetool_radiant.xml @@ -15,17 +15,21 @@ 8080 $__galaxy_url__ - > /var/log/shiny-server.log 2>&1 ]]> - + From 70d84c7d933a062ea0049394b24cf40b54315806 Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Tue, 3 Dec 2019 09:09:42 +0100 Subject: [PATCH 62/86] add input file mandatory format --- interactivetool_geoexplorer.xml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml index 894dd590c23..c5420332887 100644 --- a/interactivetool_geoexplorer.xml +++ b/interactivetool_geoexplorer.xml @@ -43,9 +43,11 @@ App: http://www.davesteps.com/geoExploreR/ .. class:: infomark +**Input data file MUST have as longitude column clomun 2, and as latitude column, column 3** + Example input file (TAB separated):: - "name" "longitude" "latitude" "countryCode" + "name" "x" "y" "countryCode" Accipiter striatus Vieillot, 1808 -60.291838 46.328137 CA Accipiter striatus Vieillot, 1808 -114.58927 35.022485 US Accipiter striatus Vieillot, 1808 -93.37406 30.00586 US From 63c7d543b0c9cc187dc9bfde09172c8fa8e474fb Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Fri, 13 Dec 2019 09:49:19 +0100 Subject: [PATCH 63/86] Fix env var name + update --- interactivetool_askomics.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml index 095d27f9f2b..94cf111a2f3 100644 --- a/interactivetool_askomics.xml +++ b/interactivetool_askomics.xml @@ -1,7 +1,7 @@ a visual SPARQL query builder - askomics/flaskomics-with-dependencies:3.1.1 + askomics/flaskomics-with-dependencies:3.2.0 @@ -19,7 +19,7 @@ ${__user_name__} $__galaxy_url__ - + prod 1 From 1d78a090d8ea0ca2ecbd94f759534698b9c83cdf Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 13 Dec 2019 17:39:57 +0100 Subject: [PATCH 64/86] add data import (#43) I was frogetting the data import part apparently :) --- interactivetool_radiant.xml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml index 769dc90f5cc..67c0205cc0e 100644 --- a/interactivetool_radiant.xml +++ b/interactivetool_radiant.xml @@ -17,6 +17,10 @@ Date: Fri, 13 Dec 2019 19:14:33 +0100 Subject: [PATCH 65/86] Copy inputdata instead of ln -s + help section update (#44) * Copy inputdata instead of ln -s * Copy inputdata instead of ln -s * Modify input datatype in help --- interactivetool_geoexplorer.xml | 18 +++++++++--------- interactivetool_radiant.xml | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml index 77375fd5725..7256cb402c2 100644 --- a/interactivetool_geoexplorer.xml +++ b/interactivetool_geoexplorer.xml @@ -19,7 +19,7 @@ diff --git a/interactivetool_radiant.xml b/interactivetool_radiant.xml index 67c0205cc0e..05b623d0ffc 100644 --- a/interactivetool_radiant.xml +++ b/interactivetool_radiant.xml @@ -19,7 +19,7 @@ Date: Tue, 17 Dec 2019 00:01:25 +0100 Subject: [PATCH 66/86] Update interactivetool_jupyter_notebook.xml --- interactivetool_jupyter_notebook.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml index 4665d48a3c3..8ecafd6f75a 100644 --- a/interactivetool_jupyter_notebook.xml +++ b/interactivetool_jupyter_notebook.xml @@ -22,7 +22,7 @@ mkdir -p ./jupyter/data && #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier)) - ln -sf '$input' './jupyter/data/${cleaned_name}' && + cp '$input' './jupyter/data/${cleaned_name}' && ## change into the directory where the notebooks are located cd ./jupyter/ && From bcf600696722b41a79db12cd9aed8edbffdc036a Mon Sep 17 00:00:00 2001 From: Yvan Le Bras Date: Fri, 20 Dec 2019 19:38:16 +0100 Subject: [PATCH 67/86] Update help and input data file type (#45) --- interactivetool_geoexplorer.xml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/interactivetool_geoexplorer.xml b/interactivetool_geoexplorer.xml index 7256cb402c2..3c8e1f5a536 100644 --- a/interactivetool_geoexplorer.xml +++ b/interactivetool_geoexplorer.xml @@ -47,18 +47,18 @@ App: http://www.davesteps.com/geoExploreR/ .. class:: infomark -**Input data file MUST have as longitude column clomun 2, and as latitude column, column 3** +**Input data file MUST have as a uniq ID per row on first column, longitude column on column 2, latitude column on column 3 and quantitative values on 4th column ** Example input file (csv):: - "name" "x" "y" "countryCode" - "Accipiter striatus Vieillot, 1808" -60.291838 46.328137 CA - "Accipiter striatus Vieillot, 1808" -114.58927 35.022485 US - "Accipiter striatus Vieillot, 1808" -93.37406 30.00586 US - "Accipiter striatus Vieillot, 1808" -79.336288 43.682218 CA - "Accipiter striatus Vieillot, 1808" -109.156024 31.904185 US - "Accipiter striatus Vieillot, 1808" -71.098031 42.297408 US - "Accipiter striatus Vieillot, 1808" -110.927215 32.18203 US +"ID" "x" "y" "test" +01 -60.291838 46.328137 2 +02 -114.58927 35.022485 3 +03 -93.37406 30.00586 4 +04 -79.336288 43.682218 5 +05 -109.156024 31.904185 2 +06 -71.098031 42.297408 9 +07 -110.927215 32.18203 12 ]]> From 4d461a5e91d24bf8d4c28aeaa95a166d765138d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 16 Jan 2020 19:28:56 +0100 Subject: [PATCH 68/86] fix jupyter --- interactivetool_jupyter_notebook.xml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml index 8ecafd6f75a..c86717460df 100644 --- a/interactivetool_jupyter_notebook.xml +++ b/interactivetool_jupyter_notebook.xml @@ -21,9 +21,10 @@ mkdir -p ./jupyter/outputs/ && mkdir -p ./jupyter/data && - #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier)) - cp '$input' './jupyter/data/${cleaned_name}' && - + #if $input: + #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier)) + cp '$input' './jupyter/data/${cleaned_name}' && + #end if ## change into the directory where the notebooks are located cd ./jupyter/ && export PATH=/home/jovyan/.local/bin:\$PATH && From 944ee259d07b060513928c131d6f94481e44cbc4 Mon Sep 17 00:00:00 2001 From: Joachim Wolff Date: Thu, 16 Jan 2020 20:58:36 +0100 Subject: [PATCH 69/86] Release 19.09 europe (#47) * Interactive tool for higlass * Changes as requested --- interactivetool_higlass.xml | 38 +++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 interactivetool_higlass.xml diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml new file mode 100644 index 00000000000..8f3231e28c4 --- /dev/null +++ b/interactivetool_higlass.xml @@ -0,0 +1,38 @@ + + an interactive Hi-C data visualizer + + higlass/higlass-docker + + + + 80 + + + + + + + + + + + + + + Interactive tool for visualising Hi-C data, works only for multi-cooler files which store multiple resolutions. + For a detailed documentaition please visit https://docs.higlass.io/. + + + + 10.1186/s13059-018-1486-1 + + + From 40640440185384998a915b7059059f3b3779ada6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 16 Jan 2020 21:44:08 +0100 Subject: [PATCH 70/86] restrict tool to mcool file --- interactivetool_higlass.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml index 8f3231e28c4..1571b811a3a 100644 --- a/interactivetool_higlass.xml +++ b/interactivetool_higlass.xml @@ -19,7 +19,7 @@ ]]> - + From 4229b1783ebee7d2228770edd30ba0d131dab0bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 22 Jan 2020 09:22:08 +0100 Subject: [PATCH 71/86] Update interactivetool_cellxgene.xml --- interactivetool_cellxgene.xml | 95 +++++++++++++++++++++++++++++++++-- 1 file changed, 90 insertions(+), 5 deletions(-) diff --git a/interactivetool_cellxgene.xml b/interactivetool_cellxgene.xml index 546bd7ab58f..3c99f3a393b 100644 --- a/interactivetool_cellxgene.xml +++ b/interactivetool_cellxgene.xml @@ -3,27 +3,112 @@ quay.io/galaxy/cellxgene-galaxy-ie:ie2 - + 80 - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + experimental_annotations['experimental_annotations_select'] == 'enable' + - Interactive tool for visualising AnnData. + An interactive explorer for single-cell transcriptomics (AnnData formatted) data + + cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas. Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data. + + Whether you need to visualize one thousand cells or one million, cellxgene helps you gain insight into your single-cell data. + https://github.com/chanzuckerberg/cellxgene + + 10.5281/zenodo.3554576 + From a93a69dc5932f6686248d24e70334ad38b073ec5 Mon Sep 17 00:00:00 2001 From: Anne Fouilloux Date: Sun, 2 Feb 2020 13:44:05 +0100 Subject: [PATCH 72/86] add panoply as new interative tool (#50) --- interactivetool_panoply.xml | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 interactivetool_panoply.xml diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml new file mode 100644 index 00000000000..6abb7b8e2c9 --- /dev/null +++ b/interactivetool_panoply.xml @@ -0,0 +1,28 @@ + + + quay.io/nordicesmhub/docker-panoply + + + + 5800 + + + + + + + + + + + + + + `Panoply `_ plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets. + + From 081dd5ec7307fec1bb1805ad3b77eee634415bb5 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 2 Feb 2020 23:24:45 +0100 Subject: [PATCH 73/86] fix panoply IT --- interactivetool_panoply.xml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml index 6abb7b8e2c9..66c18d5139f 100644 --- a/interactivetool_panoply.xml +++ b/interactivetool_panoply.xml @@ -1,4 +1,5 @@ - + + interative plotting tool for geo-referenced data quay.io/nordicesmhub/docker-panoply @@ -9,9 +10,9 @@ @@ -22,7 +23,8 @@ - + `_ plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets. + ]]> From f04a60a9b46055894b30a21212220f61dcca436c Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 3 Feb 2020 08:00:16 +0100 Subject: [PATCH 74/86] higlass changes --- interactivetool_higlass.xml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml index 1571b811a3a..20ffda8df0b 100644 --- a/interactivetool_higlass.xml +++ b/interactivetool_higlass.xml @@ -1,7 +1,7 @@ an interactive Hi-C data visualizer - higlass/higlass-docker + image-default @@ -9,13 +9,12 @@ From 85a441148f606c30242d9a614f63cf4a1ac20c78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 3 Feb 2020 23:30:14 +0100 Subject: [PATCH 75/86] Update interactivetool_higlass.xml --- interactivetool_higlass.xml | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml index 20ffda8df0b..6d0510925da 100644 --- a/interactivetool_higlass.xml +++ b/interactivetool_higlass.xml @@ -1,7 +1,7 @@ an interactive Hi-C data visualizer - image-default + quay.io/bgruening/galaxy-higlass @@ -9,19 +9,20 @@ - + - + @@ -35,3 +36,4 @@ + From 4c7c2da3bd7aa6d5c38c8cb70beea90a302db4ca Mon Sep 17 00:00:00 2001 From: Anne Fouilloux Date: Sat, 8 Feb 2020 20:26:29 +0100 Subject: [PATCH 76/86] try to fix panoply interactive tool (#51) * try to fix panoply interactive tool * add colorbars for panoply * remove colorbars moved colorbars to dockerfile. Untar colorbars.tar in the user home --- interactivetool_panoply.xml | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml index 66c18d5139f..2323bcae5c3 100644 --- a/interactivetool_panoply.xml +++ b/interactivetool_panoply.xml @@ -9,17 +9,26 @@ - + + + From bda4454671564810febbe4491a923e95d47c6344 Mon Sep 17 00:00:00 2001 From: Anne Fouilloux Date: Sat, 15 Feb 2020 12:22:19 +0100 Subject: [PATCH 77/86] update docker for interactive climate (#53) * update docker for interactive climate * test if data or not before copy --- interactivetool_climate_notebook.xml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml index aa1692ada80..0ddca7eacb8 100644 --- a/interactivetool_climate_notebook.xml +++ b/interactivetool_climate_notebook.xml @@ -1,6 +1,6 @@ - + - nordicesmhub/docker-climate-notebook:1.0 + nordicesmhub/docker-climate-notebook:1.2 @@ -21,8 +21,10 @@ mkdir -p ./jupyter/outputs/ && mkdir -p ./jupyter/data && - #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier)) - ln -sf '$input' './jupyter/data/${cleaned_name}' && + #if $input: + #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier)) + cp '$input' './jupyter/data/${cleaned_name}' && + #end if ## change into the directory where the notebooks are located cd ./jupyter/ && From 79d63abf72566c85dfdd486e587005796e78f42f Mon Sep 17 00:00:00 2001 From: Anne Fouilloux Date: Sat, 15 Feb 2020 15:01:26 +0100 Subject: [PATCH 78/86] Try to follow panoply developer recommendations (#52) * Try to follow panoply developer recommendations to fix errors * bug fix: do not fail if no png If users do not create any png files, it should not fail --- interactivetool_panoply.xml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml index 2323bcae5c3..5e84abffe8a 100644 --- a/interactivetool_panoply.xml +++ b/interactivetool_panoply.xml @@ -9,17 +9,17 @@ From 9da6e8e16952a4c0857ce92d3d52e8dfdca491f7 Mon Sep 17 00:00:00 2001 From: Anne Fouilloux Date: Sat, 22 Feb 2020 15:21:59 +0100 Subject: [PATCH 79/86] use get to copy data/notebook for jupyterlab (#54) ITs --- interactivetool_climate_notebook.xml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml index 0ddca7eacb8..f867208bfbe 100644 --- a/interactivetool_climate_notebook.xml +++ b/interactivetool_climate_notebook.xml @@ -23,7 +23,8 @@ #if $input: #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier)) - cp '$input' './jupyter/data/${cleaned_name}' && + get -t hid -i '${input.hid}' && + ln -sf '/import/${input.hid}' './jupyter/data/${cleaned_name}' && #end if ## change into the directory where the notebooks are located @@ -32,15 +33,16 @@ #if $mode.mode_select == 'scratch': ## copy default notebook - cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb && + cp '/home/jovyan/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb && jupyter trust ./ipython_galaxy_notebook.ipynb && jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True && cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook' #else: - #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier)) - cp '$mode.ipynb' ./${cleaned_name}.ipynb && - jupyter trust ./${cleaned_name}.ipynb && + #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier)) + get -t hid -i '${mode.ipynb.hid}' && + ln -sf '/import/${mode.ipynb.hid}' './jupyter/data/${cleaned_name}' && + jupyter trust ./${cleaned_name} && #if $mode.run_it: jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors ./*.ipynb && From e1a49cc678c4489e31583895fb8bd5126ebe8fd1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 22 Feb 2020 17:57:33 +0100 Subject: [PATCH 80/86] ITs --- interactivetool_climate_notebook.xml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml index f867208bfbe..d31103dfc2b 100644 --- a/interactivetool_climate_notebook.xml +++ b/interactivetool_climate_notebook.xml @@ -23,8 +23,8 @@ #if $input: #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier)) - get -t hid -i '${input.hid}' && - ln -sf '/import/${input.hid}' './jupyter/data/${cleaned_name}' && + get -t hid -i '${input.hid}' && + ln -sf '/import/${input.hid}' './jupyter/data/${cleaned_name}' && #end if ## change into the directory where the notebooks are located @@ -33,15 +33,15 @@ #if $mode.mode_select == 'scratch': ## copy default notebook - cp '/home/jovyan/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb && + cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb && jupyter trust ./ipython_galaxy_notebook.ipynb && jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True && cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook' #else: #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier)) - get -t hid -i '${mode.ipynb.hid}' && - ln -sf '/import/${mode.ipynb.hid}' './jupyter/data/${cleaned_name}' && + get -t hid -i '${mode.ipynb.hid}' && + ln -sf '/import/${mode.ipynb.hid}' './data/${cleaned_name}' jupyter trust ./${cleaned_name} && #if $mode.run_it: @@ -51,6 +51,7 @@ #end if cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook' #end if + ]]> From 16c843145fadde8789fe6ddeb3ef15f806f39dfb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 22 Feb 2020 19:32:28 +0100 Subject: [PATCH 81/86] ITs: fix commandline --- interactivetool_climate_notebook.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml index d31103dfc2b..096bc0b1ce9 100644 --- a/interactivetool_climate_notebook.xml +++ b/interactivetool_climate_notebook.xml @@ -41,7 +41,7 @@ #else: #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier)) get -t hid -i '${mode.ipynb.hid}' && - ln -sf '/import/${mode.ipynb.hid}' './data/${cleaned_name}' + ln -sf '/import/${mode.ipynb.hid}' './data/${cleaned_name}' && jupyter trust ./${cleaned_name} && #if $mode.run_it: From 0613727e9f869f9ebc5969939053705ed9f1a399 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 22 Feb 2020 20:34:19 +0100 Subject: [PATCH 82/86] ITs: fix an other path issue --- interactivetool_climate_notebook.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/interactivetool_climate_notebook.xml b/interactivetool_climate_notebook.xml index 096bc0b1ce9..2f7c989bdb1 100644 --- a/interactivetool_climate_notebook.xml +++ b/interactivetool_climate_notebook.xml @@ -42,7 +42,7 @@ #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier)) get -t hid -i '${mode.ipynb.hid}' && ln -sf '/import/${mode.ipynb.hid}' './data/${cleaned_name}' && - jupyter trust ./${cleaned_name} && + jupyter trust ./data/${cleaned_name} && #if $mode.run_it: jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors ./*.ipynb && From 38f0e3755c1a7dd8bfc952b9bbd3712bc715d332 Mon Sep 17 00:00:00 2001 From: Anne Fouilloux Date: Sun, 23 Feb 2020 00:03:13 +0100 Subject: [PATCH 83/86] Add panoply version for docker container (#55) ITs: get it working --- interactivetool_panoply.xml | 41 ++++++++++++++++++++++--------------- 1 file changed, 25 insertions(+), 16 deletions(-) diff --git a/interactivetool_panoply.xml b/interactivetool_panoply.xml index 5e84abffe8a..d663ce89b61 100644 --- a/interactivetool_panoply.xml +++ b/interactivetool_panoply.xml @@ -1,34 +1,43 @@ - + interative plotting tool for geo-referenced data + + 4.5.1 + - quay.io/nordicesmhub/docker-panoply + quay.io/nordicesmhub/docker-panoply:@VERSION@ 5800 - + output/version.txt && + cp /config/home/output/* output/ | true && + cd output && + sleep 2 && + for file in *; do mv "\$file" "\${file// /_}"; done && + for file in *; do mv "\$file" "\$file.\${file\#\#*.}"; done ]]> - - - + + + From 3a51247e8b235a0ea2dd53e1673c06002e7ce9bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 9 Mar 2020 08:52:41 +0100 Subject: [PATCH 84/86] Delete interactivetool_hicbrowser.xml --- interactivetool_hicbrowser.xml | 33 --------------------------------- 1 file changed, 33 deletions(-) delete mode 100644 interactivetool_hicbrowser.xml diff --git a/interactivetool_hicbrowser.xml b/interactivetool_hicbrowser.xml deleted file mode 100644 index 7aaa8a3e8e7..00000000000 --- a/interactivetool_hicbrowser.xml +++ /dev/null @@ -1,33 +0,0 @@ - - - bgruening/hicbrowser - - - - 80 - - - - - - - - - - - - - - Visualising HiC data with HiCBrowser. - - From 05202d52f72144cd01f78d71c28a3e5f698cda07 Mon Sep 17 00:00:00 2001 From: Alexander OSTROVSKY Date: Tue, 24 Mar 2020 09:38:09 -0700 Subject: [PATCH 85/86] adding higlass IT from eu --- tools/interactive/interactivetool_higlass.xml | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 tools/interactive/interactivetool_higlass.xml diff --git a/tools/interactive/interactivetool_higlass.xml b/tools/interactive/interactivetool_higlass.xml new file mode 100644 index 00000000000..6d0510925da --- /dev/null +++ b/tools/interactive/interactivetool_higlass.xml @@ -0,0 +1,39 @@ + + an interactive Hi-C data visualizer + + quay.io/bgruening/galaxy-higlass + + + + 80 + + + + + + + + + + + + + + Interactive tool for visualising Hi-C data, works only for multi-cooler files which store multiple resolutions. + For a detailed documentaition please visit https://docs.higlass.io/. + + + + 10.1186/s13059-018-1486-1 + + + + From 2641c692e2ed6b19dbb45a53258a3dc327071407 Mon Sep 17 00:00:00 2001 From: Alexander OSTROVSKY Date: Tue, 24 Mar 2020 10:09:00 -0700 Subject: [PATCH 86/86] migrate ITs from EU accidental files more files migrate ITs from EU accidental files more files migrate ITs from EU accidental files more files migrate ITs from EU accidental files more files --- default_notebook.ipynb | 53 -------- interactivetool_askomics.xml | 70 ----------- interactivetool_bam_iobio.xml | 47 -------- interactivetool_cellxgene.xml | 114 ------------------ interactivetool_ethercalc.xml | 63 ---------- interactivetool_higlass.xml | 39 ------ interactivetool_jupyter_notebook.xml | 94 --------------- interactivetool_neo4j.xml | 41 ------- interactivetool_phinch.xml | 39 ------ interactivetool_rstudio.xml | 74 ------------ interactivetool_wallace.xml | 67 ---------- interactivetool_wilson.xml | 56 --------- .../interactivetool_climate_notebook.xml | 0 .../interactivetool_geoexplorer.xml | 0 .../interactivetool_guacamole_desktop.xml | 0 .../interactivetool_openrefine.xml | 0 .../interactive/interactivetool_panoply.xml | 0 .../interactive/interactivetool_paraview.xml | 0 .../interactive/interactivetool_pyiron.xml | 0 .../interactive/interactivetool_radiant.xml | 0 .../interactive/interactivetool_vcf_iobio.xml | 0 21 files changed, 757 deletions(-) delete mode 100644 default_notebook.ipynb delete mode 100644 interactivetool_askomics.xml delete mode 100644 interactivetool_bam_iobio.xml delete mode 100644 interactivetool_cellxgene.xml delete mode 100644 interactivetool_ethercalc.xml delete mode 100644 interactivetool_higlass.xml delete mode 100644 interactivetool_jupyter_notebook.xml delete mode 100644 interactivetool_neo4j.xml delete mode 100644 interactivetool_phinch.xml delete mode 100644 interactivetool_rstudio.xml delete mode 100644 interactivetool_wallace.xml delete mode 100644 interactivetool_wilson.xml rename interactivetool_climate_notebook.xml => tools/interactive/interactivetool_climate_notebook.xml (100%) rename interactivetool_geoexplorer.xml => tools/interactive/interactivetool_geoexplorer.xml (100%) rename interactivetool_guacamole_desktop.xml => tools/interactive/interactivetool_guacamole_desktop.xml (100%) rename interactivetool_openrefine.xml => tools/interactive/interactivetool_openrefine.xml (100%) rename interactivetool_panoply.xml => tools/interactive/interactivetool_panoply.xml (100%) rename interactivetool_paraview.xml => tools/interactive/interactivetool_paraview.xml (100%) rename interactivetool_pyiron.xml => tools/interactive/interactivetool_pyiron.xml (100%) rename interactivetool_radiant.xml => tools/interactive/interactivetool_radiant.xml (100%) rename interactivetool_vcf_iobio.xml => tools/interactive/interactivetool_vcf_iobio.xml (100%) diff --git a/default_notebook.ipynb b/default_notebook.ipynb deleted file mode 100644 index e9573752478..00000000000 --- a/default_notebook.ipynb +++ /dev/null @@ -1,53 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Welcome to the interactive Galaxy IPython Notebook." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "You can access your data via the dataset number. Using a Python kernel, you can access dataset number 42 with ``handle = open(get(42), 'r')``.\n", - "To save data, write your data to a file, and then call ``put('filename.txt')``. The dataset will then be available in your galaxy history.\n
", - "When using a non-Python kernel, ``get`` and ``put`` are available as command-line tools, which can be accessed using system calls in R, Julia, and Ruby. For example, to read dataset number 42 into R, you can write ```handle <- file(system('get -i 42', intern = TRUE))```.\n", - "To save data in R, write the data to a file and then call ``system('put -p filename.txt')``.\n", - "Notebooks can be saved to Galaxy by clicking the large green button at the top right of the IPython interface.
\n", - "More help and informations can be found on the project [website](https://github.com/bgruening/docker-jupyter-notebook)." - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 2", - "language": "python", - "name": "python2" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.10" - } - }, - "nbformat": 4, - "nbformat_minor": 0 -} diff --git a/interactivetool_askomics.xml b/interactivetool_askomics.xml deleted file mode 100644 index 94cf111a2f3..00000000000 --- a/interactivetool_askomics.xml +++ /dev/null @@ -1,70 +0,0 @@ - - a visual SPARQL query builder - - askomics/flaskomics-with-dependencies:3.2.0 - - - - 5000 - /loginapikey/${__user_name__} - - - - - true - ${__user_name__} - Galaxy - ${__user_name__} - ${__user_email__} - ${__user_name__} - - $__galaxy_url__ - - - prod - 1 - Galaxy - AskOmics Interactive Tool for Galaxy - /tmp/askomics-it - /tmp/askomics-it/database.db - http://localhost:5000 - - true - - 85000 - 65000 - - - - - - - - - - - - - AskOmics is a visual SPARQL query interface supporting both intuitive data integration and - querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL. - - diff --git a/interactivetool_bam_iobio.xml b/interactivetool_bam_iobio.xml deleted file mode 100644 index 6c78eaa335b..00000000000 --- a/interactivetool_bam_iobio.xml +++ /dev/null @@ -1,47 +0,0 @@ - - - qiaoy/iobio-bundle.bam-iobio:1.0-ondemand - - - - 80 - - - - /tmp/app.conf && - mv /tmp/app.conf /etc/supervisor.d/app.conf && - - /usr/bin/supervisord -c /etc/supervisord.conf - ]]> - - - - - - - - - - - BAM iobio visualisation. - - diff --git a/interactivetool_cellxgene.xml b/interactivetool_cellxgene.xml deleted file mode 100644 index 3c99f3a393b..00000000000 --- a/interactivetool_cellxgene.xml +++ /dev/null @@ -1,114 +0,0 @@ - - - quay.io/galaxy/cellxgene-galaxy-ie:ie2 - - - - 80 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - experimental_annotations['experimental_annotations_select'] == 'enable' - - - - - - An interactive explorer for single-cell transcriptomics (AnnData formatted) data - - cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas. Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data. - - Whether you need to visualize one thousand cells or one million, cellxgene helps you gain insight into your single-cell data. - https://github.com/chanzuckerberg/cellxgene - - - 10.5281/zenodo.3554576 - - diff --git a/interactivetool_ethercalc.xml b/interactivetool_ethercalc.xml deleted file mode 100644 index 88676c1e997..00000000000 --- a/interactivetool_ethercalc.xml +++ /dev/null @@ -1,63 +0,0 @@ - - - shiltemann/ethercalc-galaxy-ie:17.05 - - - - 8000 - - - loading.txt - && - curl --include --request PUT --header "Content-Type: text/csv" --data-binary @loading.txt http://localhost:8000/_/galaxy - && - - ## remove dump file so this doesnt appear in audit trail - rm /dump.json - && - - ## load dataset into worksheet - curl --include --request PUT --header "Content-Type: text/csv" --data-binary @$infile http://localhost:8000/_/galaxy - && - - tail -f /etc/hosts - - ]]> - - - -&1) -while [[ \${STATUS} =~ "refused" ]] -do - echo "waiting for ethercalc: \$STATUS \n" - STATUS=\$(curl --include 'http://localhost:8000/_/galaxy' 2>&1) - sleep 2 -done - ]]> - - - - - - - - - - - - EtherCalc is a web spreadsheet. - https://ethercalc.net - - diff --git a/interactivetool_higlass.xml b/interactivetool_higlass.xml deleted file mode 100644 index 6d0510925da..00000000000 --- a/interactivetool_higlass.xml +++ /dev/null @@ -1,39 +0,0 @@ - - an interactive Hi-C data visualizer - - quay.io/bgruening/galaxy-higlass - - - - 80 - - - - - - - - - - - - - - Interactive tool for visualising Hi-C data, works only for multi-cooler files which store multiple resolutions. - For a detailed documentaition please visit https://docs.higlass.io/. - - - - 10.1186/s13059-018-1486-1 - - - - diff --git a/interactivetool_jupyter_notebook.xml b/interactivetool_jupyter_notebook.xml deleted file mode 100644 index c86717460df..00000000000 --- a/interactivetool_jupyter_notebook.xml +++ /dev/null @@ -1,94 +0,0 @@ - - - quay.io/bgruening/docker-jupyter-notebook:ie2 - - - - 8888 - ipython/lab - - - - $__history_id__ - $__galaxy_url__ - 8080 - $__galaxy_url__ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, - visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, - machine learning, and much more. - - Galaxy offers you to use Jupyter Notebooks directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to - do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter. - - You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your collegue and execute it on your dataset. - If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history. - - You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function. - - diff --git a/interactivetool_neo4j.xml b/interactivetool_neo4j.xml deleted file mode 100644 index 0b31a8b303e..00000000000 --- a/interactivetool_neo4j.xml +++ /dev/null @@ -1,41 +0,0 @@ - - - quay.io/sanbi-sa/neo_ie:3.1.9 - - - - 80 - - - - - 2345 - 2345 - false - - - - - - - - - - - - - Neo4j is a highly scalable, robust native graph database. - - diff --git a/interactivetool_phinch.xml b/interactivetool_phinch.xml deleted file mode 100644 index 382cf32f0a9..00000000000 --- a/interactivetool_phinch.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - shiltemann/docker-phinch-galaxy:16.04 - - - - 80 - - - &1 > /var/log/phinch.log - - ]]> - - - - - - - - - - - Interactive tool for visualising Biom data. - - diff --git a/interactivetool_rstudio.xml b/interactivetool_rstudio.xml deleted file mode 100644 index 63e0eb3adb0..00000000000 --- a/interactivetool_rstudio.xml +++ /dev/null @@ -1,74 +0,0 @@ - - - quay.io/erasche/docker-rstudio-notebook:19.09 - - - - 80 - rstudio/ - - - - ${__app__.security.encode_id($jupyter_notebook.history_id)} - ${__app__.config.galaxy_infrastructure_url} - 8080 - ${__app__.config.galaxy_infrastructure_url} - true - true - - #if $__user__: - #for $api_key in $__user__.api_keys: - ${api_key.key} - #break - #end for - #end if - - - - - - - - - - - - - - - - - - - - This familiar R analysis software suite will let you explore your - datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr, - LaTeX, bioconductor, cummeRbund, and many more pre-installed packages. - - Galaxy offers you to use RStudio directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to - do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in RStudio. - - The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save(). - - For example, gx_get(42) will fetch dataset 42 from your history and return the file location - - diff --git a/interactivetool_wallace.xml b/interactivetool_wallace.xml deleted file mode 100644 index 4d8e2c5353b..00000000000 --- a/interactivetool_wallace.xml +++ /dev/null @@ -1,67 +0,0 @@ - - Webbased Interactive modeling of species niches and distributions - - ylebras/wallace-docker - - - - 3838 - /sample-apps/SIG/wallace/shiny/ - - - - - ${__app__.security.encode_id($outfile.history_id)} - ${__app__.config.galaxy_infrastructure_url} - 8080 - ${__app__.config.galaxy_infrastructure_url} - - #if $__user__: - #for $api_key in $__user__.api_keys: - ${api_key.key} - #break - #end for - #end if - - - - - - - - - - - - - -`_ is a flexible platform for reproducible modeling of species niches and distributions. - -.. class:: infomark - -Example input file (TAB separated):: - - "name" "longitude" "latitude" "countryCode" - Accipiter striatus Vieillot, 1808 -60.291838 46.328137 CA - Accipiter striatus Vieillot, 1808 -114.58927 35.022485 US - Accipiter striatus Vieillot, 1808 -93.37406 30.00586 US - Accipiter striatus Vieillot, 1808 -79.336288 43.682218 CA - Accipiter striatus Vieillot, 1808 -109.156024 31.904185 US - Accipiter striatus Vieillot, 1808 -71.098031 42.297408 US - Accipiter striatus Vieillot, 1808 -110.927215 32.18203 US - -]]> - - - 10.1111/2041-210X.12945 - - diff --git a/interactivetool_wilson.xml b/interactivetool_wilson.xml deleted file mode 100644 index 7f575c43a63..00000000000 --- a/interactivetool_wilson.xml +++ /dev/null @@ -1,56 +0,0 @@ - - Webbased Interactive Omics visualization - - loosolab/wilson:2.1.1 - - - - 3838 - - - - feature_selection - true - - /home/shiny/.Renviron && - echo "WILSON_BLACKLIST_EXAMPLES=\$WILSON_BLACKLIST_EXAMPLES" >> /home/shiny/.Renviron && - ln -s ${infile} /srv/shiny-server/external_data/input.clarion && - exec shiny-server 2>&1 - ]]> - - - - - - - - - - -`_ - -.. class:: infomark - -Wilson uses the CLARION file format, which is a generic file format for quantitative comparisons of high throughput screens. - -CLARION is a data format specially developed to be used with Wilson, which relies on a tab-delimited table with -a metadata header to describe the following columns. It is based on the Summarized Experiment format and supports -all types of data which can be reduced to features and their annotation (e.g. genes, transcripts, proteins, probes) -with assigned numerical values (e.g. count, score, log2foldchange, z-score, p-value). Most result tables derived from RNA-Seq, -ChIP/ATAC-Seq, Proteomics, Microarrays, and many other analyses can thus be easily reformatted to become compatible -without having to modify the code of Wilson for each specific experiment. - -Please check the following link for details considering the `CLARION format `_. - - - -]]> - - - 10.1093/bioinformatics/bty711 - - diff --git a/interactivetool_climate_notebook.xml b/tools/interactive/interactivetool_climate_notebook.xml similarity index 100% rename from interactivetool_climate_notebook.xml rename to tools/interactive/interactivetool_climate_notebook.xml diff --git a/interactivetool_geoexplorer.xml b/tools/interactive/interactivetool_geoexplorer.xml similarity index 100% rename from interactivetool_geoexplorer.xml rename to tools/interactive/interactivetool_geoexplorer.xml diff --git a/interactivetool_guacamole_desktop.xml b/tools/interactive/interactivetool_guacamole_desktop.xml similarity index 100% rename from interactivetool_guacamole_desktop.xml rename to tools/interactive/interactivetool_guacamole_desktop.xml diff --git a/interactivetool_openrefine.xml b/tools/interactive/interactivetool_openrefine.xml similarity index 100% rename from interactivetool_openrefine.xml rename to tools/interactive/interactivetool_openrefine.xml diff --git a/interactivetool_panoply.xml b/tools/interactive/interactivetool_panoply.xml similarity index 100% rename from interactivetool_panoply.xml rename to tools/interactive/interactivetool_panoply.xml diff --git a/interactivetool_paraview.xml b/tools/interactive/interactivetool_paraview.xml similarity index 100% rename from interactivetool_paraview.xml rename to tools/interactive/interactivetool_paraview.xml diff --git a/interactivetool_pyiron.xml b/tools/interactive/interactivetool_pyiron.xml similarity index 100% rename from interactivetool_pyiron.xml rename to tools/interactive/interactivetool_pyiron.xml diff --git a/interactivetool_radiant.xml b/tools/interactive/interactivetool_radiant.xml similarity index 100% rename from interactivetool_radiant.xml rename to tools/interactive/interactivetool_radiant.xml diff --git a/interactivetool_vcf_iobio.xml b/tools/interactive/interactivetool_vcf_iobio.xml similarity index 100% rename from interactivetool_vcf_iobio.xml rename to tools/interactive/interactivetool_vcf_iobio.xml