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2d1b341fcdbdbbc4e2c24c57cd5b6a49f24bd91d
Commit Graph
2934 Commits
Author SHA1 Message Date
Alex Ostrovsky f884f9b149 Allow any format in export tool 2022-01-11 13:10:03 -08:00
Nicola Soranzo bd0cefa020 Don't use triple-quoted strings as comments 
They are expressions that get uselessly evaluated.

These were reported as B018 errors by flake8-bugbear 21.11.28 , but B018 for
strings has then been disabled in 21.11.29 since these strings can also be
used as inline attribute doc strings or module variable docstrings (not our
case though).
 2021-11-29 23:02:34 +00:00
mvdbeek 6e01abe4b2 Bump version and add profile 2021-11-26 16:18:31 +01:00
Gianmauro Cuccuru 0cf0b82959 Update interactivetool_pyiron.xml 2021-11-26 15:57:34 +01:00
Nicola Soranzo 1f8ac6c7bb Merge pull request #12965 from common-workflow-lab/type_ignore_narrow 
tighten type ignores
 2021-11-23 16:32:28 +00:00
Nicola Soranzo 30337fbd94 Merge branch 'release_21.09' into dev 2021-11-23 13:30:36 +00:00
Michael R. Crusoe 7819fdc7a6 tighten type ignores 2021-11-23 13:12:07 +01:00
Marius van den Beek 90c2f31cb4 Don't add ca-ceritificates to tool requirements 
ca-certificates is now part of the ncbi-datasets-cli conda package
 2021-11-18 17:17:19 +01:00
Marius van den BeekandHelena f1986a481f Export just once 
Thanks!

Co-authored-by: Helena <hxr@hx42.org>
 2021-11-17 15:28:07 +01:00
mvdbeek 47120ca48f Fix containerized NCBI Datasets Genomes data source tool 2021-11-12 20:17:34 +01:00
John Chilton 4fe7109ab1 Track transformations applied during uploads. 2021-11-12 10:21:55 -05:00
John Chilton 8643daf1dd Attempt to type more upload related things. 2021-11-05 11:58:53 -04:00
mvdbeek 58b2837c7c Merge branch 'release_21.09' into dev 2021-11-01 18:17:54 +01:00
mvdbeek 63e25b20f4 Set profile version of ncbi_datasets so it can run containerized 2021-10-31 16:28:38 +01:00
Dannon Baker c3605c7112 Merge remote-tracking branch 'upstream/release_21.09' into dev 2021-10-19 09:59:21 -04:00
mvdbeek 4dbf235f23 Ignore type in unused function 2021-10-12 15:25:30 +02:00
David López 2ed29639bb Merge pull request #12691 from jmchilton/more_type_fixes 
Check types of modules without type annotations in the their signatures on new modules.
 2021-10-12 13:33:17 +02:00
Nuwan Goonasekera 088c8430d1 Merge pull request #12650 from neoformit/dev-isee 
New interactive tool - iSEE
 2021-10-12 08:37:48 +05:30
John Chilton 54e8d22fa7 Check types of modules without type annotations in the their signatures on new modules. 
https://mypy.readthedocs.io/en/stable/command_line.html#cmdoption-mypy-check-untyped-defs

> it type checks the body of every function, regardless of whether it has type annotations. (By default the bodies of functions without annotations are not type checked.)
 2021-10-11 16:08:26 -04:00
Cameron Hyde 1fcef64f32 Remove redundant comment 2021-10-06 13:20:18 +10:00
Cameron Hyde c2a395b8db Merge branch 'dev' of https://github.com/neoformit/galaxy into dev-isee 2021-10-06 12:59:09 +10:00
Cameron Hyde 1039c32b72 Add interactive tool iSEE 
------

iSEE is a new interactive tool for visualizing single-cell RNAseq data. It requires a new datatype ``rdata.se`` which allows users to upload an R HDF5SummarizedExperiment object.
 2021-10-06 12:57:52 +10:00
Nate Coraor 6c39e132e7 Modernize sorter (sort1) tool: 
- Don't use shell, pipe with subprocess.PIPE instead
- Switch optparse for argparse
- Add missing coreutils requirement for `sort` command
- Change Python requirement from 2.7 to 3.8
 2021-10-01 12:47:14 -04:00
Dannon 5fac82731f Merge pull request #11738 from mvdbeek/ncbi_datasets_async_tool 
NCBI Datasets data source tool
 2021-09-20 12:17:28 -04:00
mvdbeek a10645d664 Use ncbi_genome_dataset.zip format 2021-09-13 12:05:53 +02:00
mvdbeek 947832541b Use version_command tag, single quotes for paths 2021-09-09 19:15:19 +02:00
Brad Holmes 8b77edbb53 Implement NCBI Datasets Genome Dataset server 2021-09-09 12:28:02 -04:00
Anup Kumar d46c96a63e Add tag version 2021-09-09 11:36:13 +02:00
Anup Kumar 582fb25567 Fix review comments 2021-09-09 10:25:08 +02:00
Anup Kumar 212248b3e2 Merge branch 'galaxyproject:dev' into ml-jupyter-notebook 2021-09-08 18:04:55 +02:00
Brad Holmes 0186289a63 Improve wording and target URL for NCBI Datasets Genomes link tool 2021-09-08 11:00:39 -04:00
Anup Kumar 8fbac0389f Fix review comments 2021-09-08 16:38:10 +02:00
Anup Kumar f3d042e249 Fix review comments 2021-09-08 16:36:19 +02:00
Marius van den Beek 04885b4ae2 Merge pull request #11537 from luke-c-sargent/dev 
Update bam.iobio interactive tool wrapper
 2021-09-08 13:14:53 +02:00
mvdbeek 44ee10e93d Add json_param as possible parameter type 2021-08-31 16:49:54 +02:00
mvdbeek 278b1422fd Replace taxon with generic file parameter 2021-08-31 16:45:56 +02:00
mvdbeek 58e530e65a Use separate dehydrated.zip datatype subclass 2021-08-31 16:45:56 +02:00
mvdbeek e552f79b49 Add dependency on ncbi-datasets-cli 2021-08-31 16:45:55 +02:00
mvdbeek e0855b7d9a Add simple NCBI datasets source tool 2021-08-31 16:45:55 +02:00
Marius van den BeekandNicola Soranzo 94881812a0 Tweak tool options 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-08-25 18:03:19 +03:00
mvdbeek ee63fcc736 Allow skipping sanitization of / char 
and allow using collection name as outer directory
 2021-08-25 10:51:13 +03:00
mvdbeek 1d0e8c15fa Merge branch 'release_21.05' into dev 2021-07-15 15:58:38 +02:00
mvdbeek dcac61fd1d Fix linting in grep.py script 2021-07-12 18:29:26 +02:00
mvdbeek 4eda692eae Restore Grep1 version 1.0.1 
The select option value for inverting results changed from `true` to
`-v`, so if you don't update your workflow you'll run grep without
the `-v` flag.
I don't think there's a way around this change (that is now part of
21.05 for a while, so we can't just switch the option value back).

Addresses https://github.com/galaxyproject/galaxy/issues/12249.
We should also require an additional confirmation.
 2021-07-12 18:20:43 +02:00
Anup Kumar 75aa9aaa9d Update tool 2021-06-24 16:13:08 +02:00
Anup Kumar 3a28a7d613 Update ml interactive tools 2021-06-24 15:36:49 +02:00
Anup Kumar f384154e20 Update tools 2021-06-24 15:08:56 +02:00
mvdbeek 11363a013e Merge branch 'release_21.05' into dev 2021-06-24 12:22:55 +02:00
Björn Grüning 8503ab2042 Merge pull request #12173 from mvdbeek/socket_timeout 
[21.05] Add timeout to all urlopen and requests.* methods
 2021-06-24 01:02:38 +02:00
Marius van den Beek 7177d8e88d Merge pull request #11613 from jmchilton/export_file 
Add tool for exporting individual files to galaxy file source plugins.
 2021-06-23 18:43:34 +02:00