diff --git a/tools/interactive/interactivetool_climate_notebook.xml b/tools/interactive/interactivetool_climate_notebook.xml new file mode 100644 index 00000000000..2f7c989bdb1 --- /dev/null +++ b/tools/interactive/interactivetool_climate_notebook.xml @@ -0,0 +1,116 @@ + + + nordicesmhub/docker-climate-notebook:1.2 + + + + 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. 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 + + + diff --git a/tools/interactive/interactivetool_geoexplorer.xml b/tools/interactive/interactivetool_geoexplorer.xml new file mode 100644 index 00000000000..3c8e1f5a536 --- /dev/null +++ b/tools/interactive/interactivetool_geoexplorer.xml @@ -0,0 +1,74 @@ + + An interactive spatial analysis platform using ggvis and Leaflet + + ylebras/geoexplorer-docker + + + + 3838 + /sample-apps/SIG/ + + + + $__history_id__ + $__galaxy_url__ + 8080 + $__galaxy_url__ + + + > /var/log/shiny-server.log 2>&1 + + ]]> + + + + + + + + + + +`_ is An interactive spatial analysis platform using ggvis and Leaflet. + +Author: David Stephens + +App: http://www.davesteps.com/geoExploreR/ + +.. class:: infomark + +**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):: + +"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 + +]]> + + + @misc{githubsurvey2018, + author = {davesteps}, + title = {{dashboard to visualise geographic data}}, + publisher = {Github}, + url = {https://github.com/davesteps/geoExploreR} + } + } + + diff --git a/tools/interactive/interactivetool_guacamole_desktop.xml b/tools/interactive/interactivetool_guacamole_desktop.xml new file mode 100644 index 00000000000..665f4d33eb8 --- /dev/null +++ b/tools/interactive/interactivetool_guacamole_desktop.xml @@ -0,0 +1,27 @@ + + + quay.io/bgruening/guacamole-desktop + + + + 8080 + + + + + + + + + + + + + + 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. + + 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 + + + + diff --git a/tools/interactive/interactivetool_openrefine.xml b/tools/interactive/interactivetool_openrefine.xml new file mode 100644 index 00000000000..11a0b01ffc3 --- /dev/null +++ b/tools/interactive/interactivetool_openrefine.xml @@ -0,0 +1,77 @@ + + Working with messy data + + ylebras/openrefine-docker + + + + 3333 + + + + $__history_id__ + $__galaxy_url__ + 8080 + $__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 +]]> + + + + + + + + + + + + + + + `_ (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 + +]]> + + diff --git a/tools/interactive/interactivetool_panoply.xml b/tools/interactive/interactivetool_panoply.xml new file mode 100644 index 00000000000..d663ce89b61 --- /dev/null +++ b/tools/interactive/interactivetool_panoply.xml @@ -0,0 +1,48 @@ + + interative plotting tool for geo-referenced data + + 4.5.1 + + + 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 + ]]> + + + + + + + + + + + + `_ plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets. + ]]> + + diff --git a/tools/interactive/interactivetool_paraview.xml b/tools/interactive/interactivetool_paraview.xml new file mode 100644 index 00000000000..c801600ef0e --- /dev/null +++ b/tools/interactive/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/tools/interactive/interactivetool_pyiron.xml b/tools/interactive/interactivetool_pyiron.xml new file mode 100644 index 00000000000..69caecdf71b --- /dev/null +++ b/tools/interactive/interactivetool_pyiron.xml @@ -0,0 +1,100 @@ + + + quay.io/bgruening/docker-jupyter-notebook:pyiron + + + + 8888 + ipython/lab + + + + $__history_id__ + $__galaxy_url__ + 8080 + $__galaxy_url__ + + /home/jovyan/resources + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + diff --git a/tools/interactive/interactivetool_radiant.xml b/tools/interactive/interactivetool_radiant.xml new file mode 100644 index 00000000000..05b623d0ffc --- /dev/null +++ b/tools/interactive/interactivetool_radiant.xml @@ -0,0 +1,75 @@ + + Data analytics using Radiant R Shiny app + + ylebras/radiant-docker + + + + 3838 + /sample-apps/STAT/inst/app + + + + $__history_id__ + $__galaxy_url__ + 8080 + $__galaxy_url__ + + + > /var/log/shiny-server.log 2>&1 + ]]> + + + + + + + + + + +`_ 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 + +]]> + + + @misc{githubsurvey2018, + author = {vnijs}, + title = {{Radiant - Business analytics using R and Shiny}}, + publisher = {Github}, + url = {https://github.com/vnijs/radiant} + } + } + + diff --git a/tools/interactive/interactivetool_vcf_iobio.xml b/tools/interactive/interactivetool_vcf_iobio.xml new file mode 100644 index 00000000000..3be0266c593 --- /dev/null +++ b/tools/interactive/interactivetool_vcf_iobio.xml @@ -0,0 +1,50 @@ + + + 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 + + ]]> + + + + + + + + + + `_. + +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. + ]]> + + +