Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8fa8660b25dccf62a045597bee03441b5b68b71b
https://github.com/galaxyproject/galaxy/commit/8fa8660b25dccf62a045597bee03…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M lib/galaxy/util/hash_util.py
M scripts/grt/export.py
M scripts/grt/grt.yml.sample
Log Message:
-----------
Small improvements to scripts/grt/export.py for testing.
- Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this).
- Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell.
Commit: 5f3f792f6f4ba67a2dd49e9c69b28567540c2c48
https://github.com/galaxyproject/galaxy/commit/5f3f792f6f4ba67a2dd49e9c69b2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/util/script.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/communication/communication_server.py
M scripts/db_shell.py
M scripts/galaxy-main
M scripts/grt/export.py
M scripts/grt/upload.py
M scripts/helper.py
M scripts/manage_db.py
M scripts/runtime_stats.py
M scripts/secret_decoder_ring.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
A test/integration/test_scripts.py
Log Message:
-----------
Unification of Galaxy configuration parsing for scripts/*
Commit: 16d821e12e53655947a6859a221b19a8d05eb2c4
https://github.com/galaxyproject/galaxy/commit/16d821e12e53655947a6859a221b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/sync_reports_config.py
M scripts/transfer.py
Log Message:
-----------
Mark scripts/* that don't work with YAML configuraiton options as deprecated.
Commit: 1911a55390eb4c6f9c7beb69b8f364ff6b76a119
https://github.com/galaxyproject/galaxy/commit/1911a55390eb4c6f9c7beb69b8f3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
R scripts/others/incorrect_gops_jobs.py
R scripts/others/incorrect_gops_jobs.sh
R scripts/others/incorrect_gops_join_jobs.py
R scripts/others/incorrect_gops_join_jobs.sh
Log Message:
-----------
Remove unused and unuseful scripts.
Commit: 49fed72eeab48cda9e962f2d1a678825f40842b2
https://github.com/galaxyproject/galaxy/commit/49fed72eeab48cda9e962f2d1a67…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
R scripts/data_libraries/build_lucene_index.py
R scripts/data_libraries/build_lucene_index.sh
R scripts/data_libraries/build_whoosh_index.py
R scripts/data_libraries/build_whoosh_index.sh
Log Message:
-----------
Drop data library whoosh/lucene scripts.
We don't set that config option in Galaxy anymore so these are broken anyway.
Commit: fea7953410a4145f45afbe1656735febcf390a92
https://github.com/galaxyproject/galaxy/commit/fea7953410a4145f45afbe165673…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
R scripts/cleanup_datasets/rename_purged_datasets.py
Log Message:
-----------
Remove two scripts - dataset purging hasn't worked this way for a very long time.
Commit: b14928d97203d4d459c289c393589e4f4120e3e4
https://github.com/galaxyproject/galaxy/commit/b14928d97203d4d459c289c39358…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M test/integration/test_scripts.py
Log Message:
-----------
Cleanup script integration tests.
Commit: 14e98becfe9c4d76677d9a9d0bc568c75f242bf2
https://github.com/galaxyproject/galaxy/commit/14e98becfe9c4d76677d9a9d0bc5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M lib/galaxy/util/script.py
Log Message:
-----------
Cleanup incorrect FIXME - spotted by @nsoranzo.
Commit: a177173672b86f4da8f83c3068dcb63f5f49cc40
https://github.com/galaxyproject/galaxy/commit/a177173672b86f4da8f83c3068dc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M lib/galaxy/util/script.py
Log Message:
-----------
Fix missing ENV information in config parameter args.
Commit: 8fb6aa5860344cf80c18b8fef43b43b26856ec2a
https://github.com/galaxyproject/galaxy/commit/8fb6aa5860344cf80c18b8fef43b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M lib/galaxy/util/script.py
Log Message:
-----------
Bring in @nsoranzo's requested changes for config_file_from_args, etc.
Commit: bb90ae93d810cd829ef026a3d086d51c11ac5394
https://github.com/galaxyproject/galaxy/commit/bb90ae93d810cd829ef026a3d086…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M scripts/grt/export.py
M scripts/grt/upload.py
M test/integration/test_scripts.py
Log Message:
-----------
More grt fixes - spotted by @nsoranzo.
Commit: a1f0e1772ec5280a0523f2218008933f768e886e
https://github.com/galaxyproject/galaxy/commit/a1f0e1772ec5280a0523f2218008…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M lib/galaxy/util/script.py
Log Message:
-----------
Redact help for --config-section option for @nsoranzo.
Kept the string in the file for in-code documentation but hiding it from users.
Commit: 62d4582ef6913a4c681db2a08369a7757523de42
https://github.com/galaxyproject/galaxy/commit/62d4582ef6913a4c681db2a08369…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/util/script.py
Log Message:
-----------
Touch up script unification PR based on @natefoo comments.
Commit: 4d742c3b1316aa808201c5bf3faec2587c345590
https://github.com/galaxyproject/galaxy/commit/4d742c3b1316aa808201c5bf3fae…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M Makefile
M client/README.md
Log Message:
-----------
Clarify make targets, update client/README
Commit: b960260a3449a23dc35a0f126de41c37276d8cfd
https://github.com/galaxyproject/galaxy/commit/b960260a3449a23dc35a0f126de4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Mention the client README specifically in CONTRIBUTING, to make it more obvious.
Commit: d61268cc6d58a5fbecc0399a7fe8087be45d4861
https://github.com/galaxyproject/galaxy/commit/d61268cc6d58a5fbecc0399a7fe8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Articles are important.
Commit: cbd7cb3cbcc93ef9abd651fff0760a91b5624127
https://github.com/galaxyproject/galaxy/commit/cbd7cb3cbcc93ef9abd651fff076…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Reflow text
Commit: 05584244a7a5fb8790c513d6e451ac629b2f2955
https://github.com/galaxyproject/galaxy/commit/05584244a7a5fb8790c513d6e451…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Drop old bitbucket/galaxy/galaxy-dist reference.
Commit: 96d9d0e5a236eb3fc7cf6f6612d82915fa5790e8
https://github.com/galaxyproject/galaxy/commit/96d9d0e5a236eb3fc7cf6f6612d8…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Better re-use of `tool` attribute
Commit: 4f870490f2d289b2921c422ff66e92ee5decb352
https://github.com/galaxyproject/galaxy/commit/4f870490f2d289b2921c422ff66e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Simplify get_datatype_by_extension() method
Commit: 334aea3adc975793d215f1622efc892718ecad75
https://github.com/galaxyproject/galaxy/commit/334aea3adc975793d215f1622efc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M CONTRIBUTING.md
Log Message:
-----------
Erase trello from Contributing.
Commit: 7d394d243b7d041ab357a0279e4920ab4a03fe7b
https://github.com/galaxyproject/galaxy/commit/7d394d243b7d041ab357a0279e49…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M CONTRIBUTING.md
M client/README.md
Log Message:
-----------
Proofreading - thanks @nsoranzo
Commit: d53cbe3538f186da903726ac1d00630e94cfe894
https://github.com/galaxyproject/galaxy/commit/d53cbe3538f186da903726ac1d00…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths:
M CONTRIBUTING.md
M Makefile
M client/README.md
Log Message:
-----------
Merge pull request #5800 from dannon/client_readme_clarifications
[18.01] Client related readme/makefile clarifications
Commit: 288d13b60681a3729fd38c09b41763b520239317
https://github.com/galaxyproject/galaxy/commit/288d13b60681a3729fd38c09b417…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Fix metadata setting for CRAM files
Should fix https://github.com/galaxyproject/galaxy/issues/5801.
Commit: 7e5a90cc1fd5de729e416dd249f92621f883cce8
https://github.com/galaxyproject/galaxy/commit/7e5a90cc1fd5de729e416dd249f9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M lib/galaxy/tools/repositories.py
Log Message:
-----------
Use app.datatypes_registry in ValidationContext.from_app()
Commit: d5baea1dfc1998bcba5a0083b6b94769455bc247
https://github.com/galaxyproject/galaxy/commit/d5baea1dfc1998bcba5a0083b6b9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Handle an empty datatypes_registry
Also transform it to an object attribute for re-use.
Commit: 2c4bf95c3c5416f381cd8aea210f66ffef43498d
https://github.com/galaxyproject/galaxy/commit/2c4bf95c3c5416f381cd8aea210f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/repositories.py
Log Message:
-----------
Merge pull request #5806 from nsoranzo/release_18.01_ValidationContext_fixes
[18.01] Use app.datatypes_registry in ValidationContext.from_app()
Commit: 241fadc98159f206b26938ba5626c1f24b1120c2
https://github.com/galaxyproject/galaxy/commit/241fadc98159f206b26938ba5626…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Merge pull request #5805 from mvdbeek/fix_cram_metadata
[18.01] Fix metadata setting for CRAM files
Commit: 009921387dc3f2ea0731e82fe137c7b8d06f7e8a
https://github.com/galaxyproject/galaxy/commit/009921387dc3f2ea0731e82fe137…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/script.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
R scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/communication/communication_server.py
R scripts/data_libraries/build_lucene_index.py
R scripts/data_libraries/build_lucene_index.sh
R scripts/data_libraries/build_whoosh_index.py
R scripts/data_libraries/build_whoosh_index.sh
M scripts/db_shell.py
M scripts/galaxy-main
M scripts/grt/export.py
M scripts/grt/grt.yml.sample
M scripts/grt/upload.py
M scripts/helper.py
M scripts/manage_db.py
R scripts/others/incorrect_gops_jobs.py
R scripts/others/incorrect_gops_jobs.sh
R scripts/others/incorrect_gops_join_jobs.py
R scripts/others/incorrect_gops_join_jobs.sh
M scripts/runtime_stats.py
M scripts/secret_decoder_ring.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/sync_reports_config.py
M scripts/transfer.py
A test/integration/test_scripts.py
Log Message:
-----------
Merge pull request #5769 from jmchilton/unify_scripts
[18.01] Fix scripts/ for YAML/ENV configuration processing
Commit: c9881fdc5ca751e70248e199b487e98734c39e07
https://github.com/galaxyproject/galaxy/commit/c9881fdc5ca751e70248e199b487…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-04-03 (Tue, 03 Apr 2018)
Changed paths:
M CONTRIBUTING.md
M Makefile
M client/README.md
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/repositories.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/script.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
R scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/communication/communication_server.py
R scripts/data_libraries/build_lucene_index.py
R scripts/data_libraries/build_lucene_index.sh
R scripts/data_libraries/build_whoosh_index.py
R scripts/data_libraries/build_whoosh_index.sh
M scripts/db_shell.py
M scripts/galaxy-main
M scripts/grt/export.py
M scripts/grt/grt.yml.sample
M scripts/grt/upload.py
M scripts/helper.py
M scripts/manage_db.py
R scripts/others/incorrect_gops_jobs.py
R scripts/others/incorrect_gops_jobs.sh
R scripts/others/incorrect_gops_join_jobs.py
R scripts/others/incorrect_gops_join_jobs.sh
M scripts/runtime_stats.py
M scripts/secret_decoder_ring.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/sync_reports_config.py
M scripts/transfer.py
A test/integration/test_scripts.py
Log Message:
-----------
Merge branch 'release_18.01' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/62338abbd61f...c9881fdc5ca7
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e7ecab77349ee430d4d95978c7a71c0ae54b1d77
https://github.com/galaxyproject/galaxy/commit/e7ecab77349ee430d4d95978c7a7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-04-02 (Mon, 02 Apr 2018)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
If psycopg2-binary is installed (as might be if switching between
branches), uninstalling psycopg2 will leave psycopg2-binary installed
but in a broken state. If we're removing psycopg2, we need to remove
psycopg2-binary at the same time, leaving psycopg2-binary to be
correctly installed afterwards.
Commit: 62338abbd61f7ca6b854ce0954c8cdebf2442c65
https://github.com/galaxyproject/galaxy/commit/62338abbd61f7ca6b854ce0954c8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-04-02 (Mon, 02 Apr 2018)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #5825 from dannon/psycopg2-binary-handling-touchup
psycopg2-binary handling tweak
Compare: https://github.com/galaxyproject/galaxy/compare/30337f40d4bc...62338abbd61f