opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 10:24:38 +08:00
Code Issues Packages Projects Releases Wiki Activity
44,141 Commits 62 Branches 243 Tags
e0b5097b33e89a89a9103cabd739e20bf653d5c7
Commit Graph
22438 Commits
Author SHA1 Message Date
Dannon Baker 7c6522ea3b Fixes reports app under py3 by swapping to the more standard (modern...) log configuration function 2020-02-04 08:55:46 -05:00
Dannon Baker 0688ec88a6 Prevent caching of bootstrapped client data. 2020-01-31 17:21:06 -05:00
Nicola Soranzo d525fd0913 Merge branch 'release_19.09' into release_20.01 2020-01-31 15:00:26 +00:00
Nicola Soranzo 2e587f14a7 Python3: don't check for has_key attribute 
Also partially backport commit f892231b8b .
Fix https://github.com/galaxyproject/galaxy/issues/9178 .
 2020-01-31 01:17:02 +00:00
Nicola Soranzo 230900fe85 Merge branch 'release_19.09' into release_20.01 2020-01-30 11:36:31 +00:00
Wolfgang Maier 7135ab307b Python3 compatible SnpEff and SnpSift metadata detection 2020-01-30 11:20:26 +00:00
mvdbeek cc6e2aba83 Merge branch 'release_19.09' into release_20.01 2020-01-29 22:12:27 +01:00
mvdbeek e7998dee41 Don't include build number 0 for single images 
And have conda build take precedence over image_build
for single target images.
If overriding the build suffix is really necessary one can
use the `name_override` column.
 2020-01-29 17:36:10 +01:00
mvdbeek 9a4ff7fba1 Restore parsing build numbers separated with -- 
I changed this in https://github.com/galaxyproject/galaxy/pull/9268/
but the alternative -- is also in used at https://github.com/BioContainers/multi-package-containers/blob/master/combinations/hash.tsv#L14
 2020-01-29 17:34:38 +01:00
Dannon Baker ba4e59d4ba Email notifications aren't used from just workflow steps anymore. 2020-01-29 06:20:11 -05:00
Marius van den Beek 2797857cfb Merge pull request #9170 from mvdbeek/try_sourcing_activate_d_scripts 
[20.01] source /usr/local/etc/conda/activate.d/*.sh files
 2020-01-29 10:20:39 +01:00
Dannon 8e16fcb4cc Merge pull request #9233 from dannon/external-auth-login-refinement 
[20.01] External auth login refinement
 2020-01-28 13:22:55 -05:00
Nicola Soranzo 1ce75c8297 Merge pull request #9269 from mvdbeek/fix_target_str_to_targets 
[20.01] backport 9268: Fix target_str_to_targets
 2020-01-27 18:41:19 +00:00
John Chilton 002964ee17 Merge pull request #9242 from mvdbeek/limit_dataid_in_incoming_special_case 
[19.09] Limit async hack to async tools
 2020-01-27 09:52:23 -05:00
John Chilton dbf6d3a565 Merge pull request #9234 from mvdbeek/mount_configs_rw 
[20.01] Mount job_working_directory/configs rw
 2020-01-27 09:36:57 -05:00
mvdbeek afc4ceb138 Fix target_str_to_targets 
This function is used to parse out Conda targets. The build part here is
wrong, a package build is specified like this:
`<package_name>=<version>=build`. This fixed building images as in https://github.com/BioContainers/multi-package-containers/pull/953
 2020-01-26 20:53:10 +01:00
Björn Grüning 2e1c5e427e Merge pull request #9267 from mvdbeek/mulled_build_image_name_fix 
[20.01] Fix suffix for single target mulled builds
 2020-01-25 23:45:44 +01:00
mvdbeek 4448286a75 Fix suffix for single target builds 
Without this single target builds with explicit `iamge_build`
would be called quay.io/biocontainers/<package><image_build>,
which is not right.
 2020-01-25 19:21:03 +01:00
Nicola Soranzo 6fbe8c9031 Merge branch 'release_19.09' into release_20.01 2020-01-24 17:08:02 +00:00
Nicola Soranzo d67295162a Simplify and refactor 2020-01-23 21:57:54 +00:00
mvdbeek e227b1473f Fix unselected select parameter comparison to empty string 
`$wrapper == ""` and `$wrapper == "None"` had been valid ways
to check for unselected / optional select parameters.
This restores the `$wrapper == ""` form as used by gffcompare
https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41
 2020-01-23 19:24:52 +00:00
Björn Grüning 1a6d98d29d Merge pull request #9260 from mvdbeek/fix_multi_select_equals_empty_string 
[20.01] Fix unselected select parameter comparison to empty string
 2020-01-23 19:12:28 +01:00
mvdbeek 673f21f9b6 Merge branch 'release_19.09' into release_20.01 2020-01-23 17:00:38 +01:00
mvdbeek 5d379dc4a5 Fix unselected select parameter comparison to empty string 
`$wrapper == ""` and `$wrapper == "None"` had been valid ways
to check for unselected / optional select parameters.
This restores the `$wrapper == ""` form as used by gffcompare
https://github.com/galaxyproject/tools-iuc/blob/master/tools/gffcompare/gffcompare.xml#L41
 2020-01-23 16:02:56 +01:00
Dannon Baker 1dd4a880b6 Add psa-specific user creation duplicate protection. 2020-01-22 15:57:14 -05:00
mvdbeek b7e1c1bf08 Also mkdir -p configs 2020-01-22 21:43:39 +01:00
mvdbeek 60d8c4668e Make tools that manipulate files in configs/ resubmittable 2020-01-22 19:02:23 +01:00
mvdbeek 96aabc1382 Make mounting configs dir conditional on tool profile 2020-01-22 19:02:23 +01:00
Dannon Baker 2a18857bba Swap custos auth to use standard manager-based user creation. 2020-01-22 11:43:58 -05:00
mvdbeek 7bbdf83771 Mount job_working_directory/configs rw 
Many tools have this pattern where they move the config file somewhere,
which doesn't work if it is mounted read-only.
 2020-01-22 17:40:22 +01:00
M BerntandMarius van den Beek c358e3ab69 remove space 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2020-01-22 16:54:48 +01:00
M Bernt db5bd4fac3 fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246 2020-01-22 16:16:45 +01:00
mvdbeek 54d6bad26e Merge branch 'release_19.09' into release_20.01 2020-01-22 16:08:45 +01:00
John Chilton a52e24ee3a Merge pull request #9245 from mvdbeek/fix_deletion_of_outputs_before_job 
[20.01] Fix deletion of outputs and working before job
 2020-01-22 09:02:45 -05:00
John Chilton d6a077c75e Merge pull request #9243 from mvdbeek/fix_data_table_moving 
[19.09] Fix moving of data manager output for entries
 2020-01-22 09:02:02 -05:00
Nicola Soranzo 2adf6a8f68 Merge branch 'release_19.09' into release_20.01 2020-01-22 12:24:39 +00:00
mvdbeek 8e81af2e06 Update xsd for filename attribute on configfiles 2020-01-22 11:49:06 +01:00
M BerntandMarius van den Beek 95144e5b8b Add parentheses for import 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2020-01-22 11:29:10 +01:00
mvdbeek 9e76dcd9d3 Things are nicer on python 3 2020-01-22 11:16:06 +01:00
mvdbeek 3568629c71 Ignore FileNotFoundError when deleting extra files 
This worked previously but logged an exception, causing further cleanup
to be skipped.
 2020-01-22 10:59:17 +01:00
mvdbeek 3d868e0a06 Use context manager for writing param_file 2020-01-22 10:54:49 +01:00
M Bernt 5bb2d16533 fix import order 2020-01-22 10:37:20 +01:00
mvdbeek 9a5004c5ee Place configfiles in working dir if filename set 2020-01-22 09:43:15 +01:00
mvdbeek 71788d099c Simplify PREPARE_DIRS logic 2020-01-22 09:35:57 +01:00
Dannon Baker b805aafbe6 Fix custos auth bug when the user is already signed in. 2020-01-21 14:37:24 -05:00
M Bernt be3e07fb39 fix Popen/py3 related bugs for real user setups 
- Popen returns bytes in python3
- strings are needed

analoguous to what is happening in slurm I use unicodify here
 2020-01-21 19:12:59 +01:00
mvdbeek 28277d2b67 Fix unit test 2020-01-21 11:57:20 +01:00
mvdbeek 9e4545f639 Copy working/ and outputs/ before starting job script 
This seems to be the most robust way to make sure that resubmission by
the DRM will start with proper configfiles and pre-populated outputs
(OutputParameterJSONTool).
The cost should be minimal as most of the time these are empty
directories.
This would also help with https://github.com/galaxyproject/galaxy/pull/9236#issuecomment-576050103
 2020-01-21 11:18:23 +01:00
mvdbeek 8d099ef98b Only delete writable files on job resubmission 2020-01-21 11:18:13 +01:00
mvdbeek db472b2bc0 Only delete working/ and outputs on resubmission 2020-01-21 11:16:38 +01:00