galaxy-commits
Threads by month
- ----- 2025 -----
- July
- June
- May
- April
- March
- February
- January
- ----- 2024 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2023 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2022 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2021 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2020 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2019 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2018 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2017 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2016 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2015 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2014 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2013 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2012 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2011 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2010 -----
- December
- November
- October
- September
- August
- July
- June
- May
February 2017
- 1 participants
- 133 discussions
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 2bce4225a8d87f21350040eaff122c79e5aec1ab
https://github.com/galaxyproject/usegalaxy-playbook/commit/2bce4225a8d87f21…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M stage/galaxy_version.yml
Log Message:
-----------
Update test.
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c3650d9fb6b2c422d62db1c10c4bfffe425e5f36
https://github.com/galaxyproject/galaxy/commit/c3650d9fb6b2c422d62db1c10c4b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-26 (Thu, 26 Jan 2017)
Changed paths:
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
Log Message:
-----------
add initial release notes
Commit: 1fe0f2f76b67bbb034af48e0ee963da4dd176284
https://github.com/galaxyproject/galaxy/commit/1fe0f2f76b67bbb034af48e0ee96…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01.rst
Log Message:
-----------
bring in @nsoranzo's comments
Commit: 47863ff13444b1596e12fb4903229717593bdea4
https://github.com/galaxyproject/galaxy/commit/47863ff13444b1596e12fb490322…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
M doc/source/releases/_thanks.rst
Log Message:
-----------
more work towards reasonable release notes
Commit: 21525ee25ef2b7b49733d845affe6fd9ede5b7b2
https://github.com/galaxyproject/galaxy/commit/21525ee25ef2b7b49733d845affe…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
clarify fastq compression handling
Commit: e0d2f6dbc8b8bc5d96855cc74bf62fa56c731fd6
https://github.com/galaxyproject/galaxy/commit/e0d2f6dbc8b8bc5d96855cc74bf6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
clarify how to prevent unpacking of archives
Commit: 2d2e7ddc958f9908fa72caca540c333929e8b517
https://github.com/galaxyproject/galaxy/commit/2d2e7ddc958f9908fa72caca540c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
Don't encourage uploads of fastq in release notes.
My understanding is nearly all data now produced is fastqsanger.
Commit: 32e624195b827b1e3ba607337c1b87067651b0c2
https://github.com/galaxyproject/galaxy/commit/32e624195b827b1e3ba607337c1b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
Add all PRs and authors for compressed fastq support
Commit: 76076dfeff8de4eb9509e60563a6cc905d2b5b22
https://github.com/galaxyproject/galaxy/commit/76076dfeff8de4eb9509e60563a6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
remove jmchilton from credits
the Galaxy-lab members are explicitly omitted from RN mentions
Commit: 9217889d2e23d339665a95a06d97112a28e91b2b
https://github.com/galaxyproject/galaxy/commit/9217889d2e23d339665a95a06d97…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
Add ashvark to author list
Commit: 2f0a635e9f270007ec1da64b7ed054ff47cbb35e
https://github.com/galaxyproject/galaxy/commit/2f0a635e9f270007ec1da64b7ed0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01.rst
Log Message:
-----------
Various improvements to the release notes.
- Rewording things to focus on reader concerns.
- Grouping things into single bullets (like testing stuff) and close to similar topics (like Conda stuff).
- Eliminated some things which should have been marked #minor
Commit: e3f50e90f8ab9e8313d077da2961a81bafb7c90a
https://github.com/galaxyproject/galaxy/commit/e3f50e90f8ab9e8313d077da2961…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
More work on 17.01 release notes.
Commit: f985b613ea1002a6595e073dfb459880ad7fdfdf
https://github.com/galaxyproject/galaxy/commit/f985b613ea1002a6595e073dfb45…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
Log Message:
-----------
Fix new history naming for batchmode workflow runs
Commit: 639e2e5b2c4631901450a58710acbee373b498d8
https://github.com/galaxyproject/galaxy/commit/639e2e5b2c4631901450a58710ac…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
minor tweaks of RN
Commit: 715e73adc97ea2c88639a50d1aaf88b9a1f3bcdc
https://github.com/galaxyproject/galaxy/commit/715e73adc97ea2c88639a50d1aaf…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M doc/source/releases/17.01.rst
Log Message:
-----------
minor changes thanks to @nsoranzo
Commit: 4df803a930c1546d41e4adeef9a0cc286cf6ada0
https://github.com/galaxyproject/galaxy/commit/4df803a930c1546d41e4adeef9a0…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
Log Message:
-----------
Merge pull request #3532 from guerler/fix_new_history_naming
[16.10] Fix new history naming for batchmode workflow runs
Commit: f9edf39f58b9942b461e5238c9df60ab5765faea
https://github.com/galaxyproject/galaxy/commit/f9edf39f58b9942b461e5238c9df…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
Migrate galaxy_utils to a wheel.
Alternative approach to #3542 which was not future proof with Conda dependencies. I think this should be now.
xref #3364 #2994 http://dev.list.galaxyproject.org/Tools-using-Galaxy-s-Python-library-td467…
Rebased with fixes from @nsoranzo and @mvdbeek.
Commit: 934bf6b056bc2475b217d62524e95de564c7a7a8
https://github.com/galaxyproject/galaxy/commit/934bf6b056bc2475b217d62524e9…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Ensure toolbox conf watcher updates cached hash when config change is
detected
Commit: b41b8e305bac3425b9bd20cda43936b23bd02abd
https://github.com/galaxyproject/galaxy/commit/b41b8e305bac3425b9bd20cda439…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Merge pull request #3558 from natefoo/toolconf-watch-hash
[16.10] Ensure toolbox conf watcher updates cached hash when config change is detected
Commit: 43873b8a6de5a6f1669f8364fff54c206b5f2f84
https://github.com/galaxyproject/galaxy/commit/43873b8a6de5a6f1669f8364fff5…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Merge pull request #3560 from galaxyproject/release_16.10
[17.01] Merge 16.10 into 17.01
Commit: 16a97e47c70f544d7acd30aac107a6687f01b736
https://github.com/galaxyproject/galaxy/commit/16a97e47c70f544d7acd30aac107…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
Merge pull request #3551 from jmchilton/galaxy_utils_external
[17.01] Migrate galaxy_utils to a wheel.
Commit: 9feb8b3f02038c5cadad858d4b4675467ec90616
https://github.com/galaxyproject/galaxy/commit/9feb8b3f02038c5cadad858d4b46…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
M doc/source/releases/_thanks.rst
Log Message:
-----------
Merge pull request #3497 from martenson/17.01_release_notes
[17.01] add release notes
Commit: 440c75fe589d3c92e6837bdd244490dc29003e45
https://github.com/galaxyproject/galaxy/commit/440c75fe589d3c92e6837bdd2444…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
M doc/source/releases/_thanks.rst
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/toolbox/watcher.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
Merge branch 'release_17.01' into dev
Commit: 6fc64f6f46f16efb45450cf4597d5e86dec865b5
https://github.com/galaxyproject/galaxy/commit/6fc64f6f46f16efb45450cf4597d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
M doc/source/releases/_thanks.rst
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/toolbox/watcher.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
Merge pull request #3565 from dannon/merge_1701_dev
Merge 1701 to dev
Compare: https://github.com/galaxyproject/galaxy/compare/ed98b1b75aac...6fc64f6f46f1
1
0
[galaxyproject/galaxy] a391af: Remove duplicated/unused display_migration_details...
by GitHub 06 Feb '17
by GitHub 06 Feb '17
06 Feb '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a391af968742ab616f98edf7b889fe639302cf00
https://github.com/galaxyproject/galaxy/commit/a391af968742ab616f98edf7b889…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
Log Message:
-----------
Remove duplicated/unused display_migration_details() functions
Also fix import order.
Commit: ed98b1b75aacc676d0f43a0a3a519132756518b7
https://github.com/galaxyproject/galaxy/commit/ed98b1b75aacc676d0f43a0a3a51…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
Log Message:
-----------
Merge pull request #3564 from nsoranzo/remove_display_migration_details
Remove duplicated/unused display_migration_details() functions
Compare: https://github.com/galaxyproject/galaxy/compare/900c8d2dfe5e...ed98b1b75aac
1
0
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: c3650d9fb6b2c422d62db1c10c4bfffe425e5f36
https://github.com/galaxyproject/galaxy/commit/c3650d9fb6b2c422d62db1c10c4b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-26 (Thu, 26 Jan 2017)
Changed paths:
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
Log Message:
-----------
add initial release notes
Commit: 1fe0f2f76b67bbb034af48e0ee963da4dd176284
https://github.com/galaxyproject/galaxy/commit/1fe0f2f76b67bbb034af48e0ee96…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01.rst
Log Message:
-----------
bring in @nsoranzo's comments
Commit: 47863ff13444b1596e12fb4903229717593bdea4
https://github.com/galaxyproject/galaxy/commit/47863ff13444b1596e12fb490322…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
M doc/source/releases/_thanks.rst
Log Message:
-----------
more work towards reasonable release notes
Commit: 21525ee25ef2b7b49733d845affe6fd9ede5b7b2
https://github.com/galaxyproject/galaxy/commit/21525ee25ef2b7b49733d845affe…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
clarify fastq compression handling
Commit: e0d2f6dbc8b8bc5d96855cc74bf62fa56c731fd6
https://github.com/galaxyproject/galaxy/commit/e0d2f6dbc8b8bc5d96855cc74bf6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
clarify how to prevent unpacking of archives
Commit: 2d2e7ddc958f9908fa72caca540c333929e8b517
https://github.com/galaxyproject/galaxy/commit/2d2e7ddc958f9908fa72caca540c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
Don't encourage uploads of fastq in release notes.
My understanding is nearly all data now produced is fastqsanger.
Commit: 32e624195b827b1e3ba607337c1b87067651b0c2
https://github.com/galaxyproject/galaxy/commit/32e624195b827b1e3ba607337c1b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
Add all PRs and authors for compressed fastq support
Commit: 76076dfeff8de4eb9509e60563a6cc905d2b5b22
https://github.com/galaxyproject/galaxy/commit/76076dfeff8de4eb9509e60563a6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
remove jmchilton from credits
the Galaxy-lab members are explicitly omitted from RN mentions
Commit: 9217889d2e23d339665a95a06d97112a28e91b2b
https://github.com/galaxyproject/galaxy/commit/9217889d2e23d339665a95a06d97…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
Add ashvark to author list
Commit: 2f0a635e9f270007ec1da64b7ed054ff47cbb35e
https://github.com/galaxyproject/galaxy/commit/2f0a635e9f270007ec1da64b7ed0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01.rst
Log Message:
-----------
Various improvements to the release notes.
- Rewording things to focus on reader concerns.
- Grouping things into single bullets (like testing stuff) and close to similar topics (like Conda stuff).
- Eliminated some things which should have been marked #minor
Commit: e3f50e90f8ab9e8313d077da2961a81bafb7c90a
https://github.com/galaxyproject/galaxy/commit/e3f50e90f8ab9e8313d077da2961…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
More work on 17.01 release notes.
Commit: 639e2e5b2c4631901450a58710acbee373b498d8
https://github.com/galaxyproject/galaxy/commit/639e2e5b2c4631901450a58710ac…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
Log Message:
-----------
minor tweaks of RN
Commit: 715e73adc97ea2c88639a50d1aaf88b9a1f3bcdc
https://github.com/galaxyproject/galaxy/commit/715e73adc97ea2c88639a50d1aaf…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M doc/source/releases/17.01.rst
Log Message:
-----------
minor changes thanks to @nsoranzo
Commit: 9feb8b3f02038c5cadad858d4b4675467ec90616
https://github.com/galaxyproject/galaxy/commit/9feb8b3f02038c5cadad858d4b46…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
M doc/source/releases/_thanks.rst
Log Message:
-----------
Merge pull request #3497 from martenson/17.01_release_notes
[17.01] add release notes
Compare: https://github.com/galaxyproject/galaxy/compare/16a97e47c70f...9feb8b3f0203
1
0
06 Feb '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5ee67b0f2d586f6af9416d27a839a900b3864a0f
https://github.com/galaxyproject/galaxy/commit/5ee67b0f2d586f6af9416d27a839…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Implement automatic tool_data_table reload
if *.loc files have been modified.
Commit: 732e2966329b77c61da4a992750aeeba326fca81
https://github.com/galaxyproject/galaxy/commit/732e2966329b77c61da4a992750a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Replace all LocDir and loc_dir related variable names with ToolDataDir or tool_data_dir (thanks @nsoranzo)
Commit: a48f97ae1bb4bd4c9515e85c59afc7f5b1cc1ba7
https://github.com/galaxyproject/galaxy/commit/a48f97ae1bb4bd4c9515e85c59af…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Activate recursive watching for tool datat dir since toolshed datamanager tables are in subdirectory
Commit: 900c8d2dfe5ee687b8926c55a6d1a701c5049113
https://github.com/galaxyproject/galaxy/commit/900c8d2dfe5ee687b8926c55a6d1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Merge pull request #3533 from mvdbeek/tdt_reload
Watch tool data table *.loc files, and reload if modified.
Compare: https://github.com/galaxyproject/galaxy/compare/d62824892ccf...900c8d2dfe5e
1
0
[galaxyproject/galaxy] ea013f: add a task to protect the release branch in github
by GitHub 06 Feb '17
by GitHub 06 Feb '17
06 Feb '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ea013fefa82ea6454168feda71be7e589e3b162d
https://github.com/galaxyproject/galaxy/commit/ea013fefa82ea6454168feda71be…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
add a task to protect the release branch in github
to the release process
should prevent https://github.com/galaxyproject/galaxy/pull/3560#issuecomment-277520315
thanks @nsoranzo
Commit: 2392bb90624273a6288b720819a6816c945a0cc1
https://github.com/galaxyproject/galaxy/commit/2392bb90624273a6288b720819a6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
A .ci/jenkins/api/run_tests.sh
A .ci/jenkins/framework/run_tests.sh
A .ci/jenkins/integration/run_tests.sh
A .ci/jenkins/selenium/Dockerfile
A .ci/jenkins/selenium/docker-compose.yml
A .ci/jenkins/selenium/galaxy.ini
A .ci/jenkins/selenium/run_galaxy.bash
A .ci/jenkins/selenium/run_tests.sh
A .ci/jenkins/toolshed/run_tests.sh
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M Makefile
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
A client/galaxy/scripts/mvc/user/user-preferences.js
A client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
A client/galaxy/scripts/mvc/workflow/workflow-icons.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
A config/build_sites.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/local_conda_mapping.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.xml
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/sample.txt
R config/plugins/visualizations/charts/static/app.css
R config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/example/config.js
R config/plugins/visualizations/charts/static/charts/others/example/logo.png
R config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
R config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/types.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/client/app.css
A config/plugins/visualizations/charts/static/client/app.js
A config/plugins/visualizations/charts/static/client/components/model.js
A config/plugins/visualizations/charts/static/client/components/screenshot.js
A config/plugins/visualizations/charts/static/client/views/description.js
A config/plugins/visualizations/charts/static/client/views/editor.js
A config/plugins/visualizations/charts/static/client/views/groups.js
A config/plugins/visualizations/charts/static/client/views/settings.js
A config/plugins/visualizations/charts/static/client/views/viewer.js
A config/plugins/visualizations/charts/static/client/views/viewport.js
R config/plugins/visualizations/charts/static/components/jobs.js
R config/plugins/visualizations/charts/static/components/model.js
R config/plugins/visualizations/charts/static/components/screenshot.js
R config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js
R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js
R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.barRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.blockRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.boxplotRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasOverlay.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasTextRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.categoryAxisRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map
A config/plugins/visualizations/charts/static/repository/build/others_example.js
A config/plugins/visualizations/charts/static/repository/build/others_example.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.js
A config/plugins/visualizations/charts/static/repository/build/registry.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
A config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
A config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/jobs.js
A config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/static/views/description.js
R config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/groups.js
R config/plugins/visualizations/charts/static/views/settings.js
R config/plugins/visualizations/charts/static/views/types.js
R config/plugins/visualizations/charts/static/views/viewer.js
R config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
A config/plugins/visualizations/charts/webpack.config.js
M config/plugins/visualizations/csg/templates/csg.mako
M config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
M config/tool_conf.xml.sample
M config/tool_data_table_conf.xml.sample
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
A display_applications/igv/genome_fasta.xml
M doc/Makefile
A doc/fix_schema_rst.sh
M doc/parse_gx_xsd.py
M doc/patch.py
M doc/schema_template.md
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
A doc/source/admin/images_webhooks/history-menu.png
A doc/source/admin/images_webhooks/masthead.png
A doc/source/admin/images_webhooks/masthead_trans_object.png
A doc/source/admin/images_webhooks/tool.png
A doc/source/admin/images_webhooks/workflow.png
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/admin/interactive_environments.svg
R doc/source/admin/interactive_environments_success.png
A doc/source/admin/mulled_containers.rst
A doc/source/admin/webhooks.rst
M doc/source/api/guidelines.rst
M doc/source/conf.py
M doc/source/dev/build_a_job_runner.rst
M doc/source/dev/faq.rst
M doc/source/dev/index.rst
A doc/source/dev/inherit.png
M doc/source/dev/interactive_environments.rst
A doc/source/dev/interactive_environments_success.png
A doc/source/dev/queue.png
A doc/source/dev/queue_b.png
A doc/source/dev/runner_diag.png
M doc/source/index.rst
M doc/source/lib/galaxy.datatypes.converters.rst
M doc/source/lib/galaxy.jobs.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.tools.linters.rst
M doc/source/lib/galaxy.tools.parameters.rst
R doc/source/lib/galaxy.util.backports.importlib.rst
M doc/source/lib/galaxy.util.backports.rst
M doc/source/lib/galaxy.util.rst
M doc/source/project/issues.rst
M doc/source/project/organization.rst
M doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
M doc/source/releases/16.07.rst
A doc/source/releases/16.10.rst
M doc/source/releases/16.10_announce.rst
A doc/source/releases/17.01_announce.rst
M doc/source/releases/index.rst
A doc/source/slideshow/architecture/galaxy_architecture.md
A doc/source/slideshow/architecture/images/backbone-model-view.svg
A doc/source/slideshow/architecture/images/cluster_support.svg
A doc/source/slideshow/architecture/images/data_managers.svg
A doc/source/slideshow/architecture/images/docker-chart.png
A doc/source/slideshow/architecture/images/family/team.png
A doc/source/slideshow/architecture/images/galaxy_schema.png
A doc/source/slideshow/architecture/images/hda.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt
A doc/source/slideshow/architecture/images/jsload.png
A doc/source/slideshow/architecture/images/libraries.svg
A doc/source/slideshow/architecture/images/library_permissions.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.txt
A doc/source/slideshow/architecture/images/objectstore_diagram.svg
A doc/source/slideshow/architecture/images/plantuml_options.txt
A doc/source/slideshow/architecture/images/sequence.json
A doc/source/slideshow/architecture/images/server_client.plantuml.svg
A doc/source/slideshow/architecture/images/server_client.plantuml.txt
A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt
A doc/source/slideshow/architecture/images/sqla_arch_small.png
A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg
A doc/source/slideshow/architecture/images/usegalaxyorg.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.txt
A doc/source/slideshow/architecture/images/what-is-webpack.svg
A doc/source/slideshow/architecture/images/workflow_definition.svg
A doc/source/slideshow/architecture/images/workflow_run.svg
A doc/source/slideshow/architecture/images/wsgi_app.svg
A doc/source/slideshow/architecture/images/wsgi_request.svg
A doc/source/slideshow/architecture/remark-latest.min.js
A doc/source/slideshow/architecture/style.css
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/__init__.py
M lib/galaxy/auth/providers/alwaysreject.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/localdb.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bam_to_bai.xml
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
A lib/galaxy/datatypes/converters/fasta_to_fai.xml
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fasta_to_len.xml
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml
A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml
A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml
A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml
A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml
A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml
A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml
A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml
A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_coverage.xml
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/len_to_linecount.xml
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/sam_to_bam.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/1.smat
A lib/galaxy/datatypes/test/diamond_db.dmnd
A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
A lib/galaxy/datatypes/test/test.CEL
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/triples.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/datasets.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
A lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/runners/util/__init__.py
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/job/__init__.py
M lib/galaxy/jobs/runners/util/cli/job/slurm.py
M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
M lib/galaxy/jobs/runners/util/cli/shell/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/jobs/runners/util/condor/__init__.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/runners/util/kill.py
M lib/galaxy/jobs/runners/util/retry.py
M lib/galaxy/jobs/runners/util/sudo.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/managers/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/pulsar.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/queue_worker.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/data_manager.py
M lib/galaxy/tools/actions/data_source.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/dependencies.py
M lib/galaxy/tools/deps/docker_util.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/input_translation.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/filters/examples.py.sample
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/verify/asserts/text.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/aliaspickler.py
M lib/galaxy/util/checkers.py
A lib/galaxy/util/compression_utils.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/util/hash_util.py
A lib/galaxy/util/image_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/object_wrapper.py
A lib/galaxy/util/oset.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/util/topsort.py
M lib/galaxy/version.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/__init__.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/js/Dockerfile
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/api/users.py
A lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/search.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/__init__.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/__init__.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
A lib/galaxy/webhooks/__init__.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/schedulers/__init__.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/galaxy/workflow/steps.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/sequence.py
M lib/galaxy_utils/sequence/vcf.py
M lib/mimeparse.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/repository_types/unrestricted.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_util.py
M run.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/filter_failed_datasets_from_collection.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/reset_metadata_on_installed_repositories.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/auth/pam_auth_helper.py
M scripts/bootstrap_history.py
R scripts/bootstrap_history_announce_template.rst
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_galaxy.py
M scripts/check_python.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/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/communication/communication_server.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
A scripts/dump_tour.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/functional_tests.py
M scripts/galaxy-main
M scripts/grt.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
A scripts/manage_tool_dependencies.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
R scripts/run_selenium_tests.sh
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
A scripts/slideshow/__init__.py
A scripts/slideshow/build_slideshow.py
A scripts/slideshow/example.md
A scripts/slideshow/slideshow_template.html
A scripts/slideshow/style.sample.css
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/add_repository_registry_entry.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/remove_repository_registry_entry.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M setup.cfg
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
A static/maps/libs/showdown.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
A static/maps/mvc/tool/tool-webhooks.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-tabs.js.map
A static/maps/mvc/ui/ui-thumbnails.js.map
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-row.js.map
A static/maps/mvc/user/change-password.js.map
A static/maps/mvc/user/extra-information.js.map
A static/maps/mvc/user/manage-user-information.js.map
A static/maps/mvc/user/user-preferences.js.map
A static/maps/mvc/webhooks.js.map
M static/maps/mvc/workflow/workflow-canvas.js.map
A static/maps/mvc/workflow/workflow-icons.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
A static/scripts/libs/showdown.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
A static/scripts/mvc/tool/tool-webhooks.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-tabs.js
A static/scripts/mvc/ui/ui-thumbnails.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
A static/scripts/mvc/user/change-password.js
A static/scripts/mvc/user/extra-information.js
A static/scripts/mvc/user/manage-user-information.js
A static/scripts/mvc/user/user-preferences.js
A static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-canvas.js
A static/scripts/mvc/workflow/workflow-icons.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/utils/utils.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M static/welcome.html.sample
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/ind_share_base.mako
M templates/show_params.mako
R templates/user/change_password.mako
R templates/user/communication_settings.mako
R templates/user/edit_address.mako
M templates/user/index.mako
R templates/user/new_address.mako
R templates/user/permissions.mako
M templates/user/register.mako
R templates/user/toolbox_filters.mako
R templates/user/username.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/history/share.mako
M templates/webapps/galaxy/library/common/common.mako
R templates/webapps/galaxy/user/api_keys.mako
M templates/webapps/galaxy/user/list_users.mako
R templates/webapps/galaxy/user/manage_info.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/editor_generic_form.mako
R templates/webapps/galaxy/workflow/editor_tool_form.mako
R templates/webapps/galaxy/workflow/index.mako
M templates/webapps/galaxy/workflow/list.mako
R templates/webapps/galaxy/workflow/missing_tools.mako
R templates/webapps/galaxy/workflow/myexp_export_content.mako
R templates/webapps/galaxy/workflow/rename.mako
M templates/webapps/tool_shed/repository/common.mako
A templates/webapps/tool_shed/user/api_keys.mako
A templates/webapps/tool_shed/user/change_password.mako
A templates/webapps/tool_shed/user/index.mako
A templates/webapps/tool_shed/user/username.mako
A test-data/1.fastqsanger.bz2
A test-data/1.fastqsanger.gz
A test-data/bam_from_sam.bam
A test-data/sam_with_header.sam
A test-data/simple.xml
R test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
A test/api/test_configuration.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_history_contents_provenance.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_search.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_visualizations.py
A test/api/test_webhooks.py
R test/api/test_workflow_1.ga
R test/api/test_workflow_2.ga
M test/api/test_workflow_extraction.py
R test/api/test_workflow_map_reduce_pause.ga
R test/api/test_workflow_matching_lists.ga
R test/api/test_workflow_missing_tool.ga
R test/api/test_workflow_pause.ga
R test/api/test_workflow_topoambigouity.ga
R test/api/test_workflow_topoambigouity_auto_laidout.ga
R test/api/test_workflow_validation_1.ga
R test/api/test_workflow_with_runtime_input.ga
M test/api/test_workflows.py
R test/api/workflows_format_2/README.txt
R test/api/workflows_format_2/__init__.py
R test/api/workflows_format_2/converter.py
R test/api/workflows_format_2/interface.py
R test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/api_asserts.py
A test/base/data/test_workflow_1.ga
A test/base/data/test_workflow_2.ga
A test/base/data/test_workflow_batch.ga
A test/base/data/test_workflow_map_reduce_pause.ga
A test/base/data/test_workflow_matching_lists.ga
A test/base/data/test_workflow_missing_tool.ga
A test/base/data/test_workflow_pause.ga
A test/base/data/test_workflow_topoambigouity.ga
A test/base/data/test_workflow_topoambigouity_auto_laidout.ga
A test/base/data/test_workflow_validation_1.ga
A test/base/data/test_workflow_with_runtime_input.ga
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
A test/base/populators.py
M test/base/test_logging.py
M test/base/twilltestcase.py
A test/base/workflows_format_2/README.txt
A test/base/workflows_format_2/__init__.py
A test/base/workflows_format_2/converter.py
A test/base/workflows_format_2/interface.py
A test/base/workflows_format_2/main.py
R test/casperjs/anon-history-tests.js
R test/casperjs/api-batch-tests.js
R test/casperjs/api-configuration-tests.js
R test/casperjs/api-dataset-tests.js
R test/casperjs/api-history-tests.js
R test/casperjs/api-tool-tests.js
R test/casperjs/api-user-tests.js
R test/casperjs/api-visualizations-tests.js
R test/casperjs/hda-state-tests.js
R test/casperjs/history-options-tests.js
R test/casperjs/history-panel-tests.js
R test/casperjs/history-share-tests.js
R test/casperjs/login-tests.js
R test/casperjs/registration-tests.js
R test/casperjs/upload-tests.js
M test/docker/README.md
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/tools/checksum.xml
A test/functional/tools/color_param.xml
M test/functional/tools/column_param.xml
A test/functional/tools/compressed_bz2_fastq_conversion.xml
A test/functional/tools/compressed_bz2_fastq_no_conversion.xml
A test/functional/tools/compressed_gz_fastq_conversion.xml
A test/functional/tools/compressed_gz_fastq_no_conversion.xml
A test/functional/tools/explicit_conversion.xml
A test/functional/tools/for_tours/filtering.py
A test/functional/tools/for_tours/filtering.xml
A test/functional/tools/for_workflows/mapper2.xml
A test/functional/tools/implicit_conversion.xml
A test/functional/tools/is_valid_xml.xml
A test/functional/tools/legacy_r.xml
M test/functional/tools/md5sum.xml
A test/functional/tools/metadata_column_names.xml
A test/functional/tools/mulled_example_conflict.xml
A test/functional/tools/mulled_example_multi_1.xml
A test/functional/tools/multi_data_optional.xml
A test/functional/tools/paired_collection_map_over_structured_like.xml
A test/functional/tools/param_text_option.xml
A test/functional/tools/python_environment_problem.py
A test/functional/tools/python_environment_problem.xml
A test/functional/tools/sam_to_bam.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/version_command.py
A test/functional/tools/version_command_interpreter.xml
A test/functional/tools/version_command_plain.xml
A test/functional/tools/version_command_tool_dir.xml
A test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/config/phdcomics.yaml
A test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/static/script.js
A test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/trans_object/config/trans_object.yaml
A test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/static/script.js
A test/functional/webhooks/xkcd/static/styles.css
R test/functional/workflow.py
A test/galaxy_selenium/__init__.py
A test/galaxy_selenium/cli.py
A test/galaxy_selenium/data.py
A test/galaxy_selenium/driver_factory.py
A test/galaxy_selenium/has_driver.py
A test/galaxy_selenium/navigates_galaxy.py
A test/galaxy_selenium/navigation-data.yml
A test/galaxy_selenium/sizzle.py
A test/integration/resubmission_default_job_conf.xml
A test/integration/resubmission_job_conf.xml
A test/integration/resubmission_job_resource_parameters_conf.xml
A test/integration/resubmission_rules/__init__.py
A test/integration/resubmission_rules/rules.py
A test/integration/resubmission_runners.py
A test/integration/test_job_resubmission.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/qunit/package.json
M test/qunit/tests/ui_tests.js
M test/qunit/tests/workflow_editor_tests.js
A test/selenium_tests/__init__.py
A test/selenium_tests/_workflow_fixtures.py
A test/selenium_tests/framework.py
A test/selenium_tests/test_anon_history.py
A test/selenium_tests/test_history_dataset_state.py
A test/selenium_tests/test_history_options.py
A test/selenium_tests/test_history_panel.py
A test/selenium_tests/test_history_sharing.py
A test/selenium_tests/test_login.py
A test/selenium_tests/test_registration.py
A test/selenium_tests/test_stock_tours.py
A test/selenium_tests/test_tool_form.py
A test/selenium_tests/test_uploads.py
A test/selenium_tests/test_workflow_editor.py
A test/selenium_tests/test_workflow_management.py
A test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/test_sockets.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/evolution/add_scores.xml
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
R tools/filters/gff/sort_gtf.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/pasteWrapper.xml
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.py
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/macros.xml
M tools/maf/maf_by_block_number.py
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.py
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.py
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.py
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.py
M tools/maf/vcf_to_maf_customtrack.xml
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.py
M tools/metag_tools/shrimp_wrapper.xml
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/fastq_gen_conv.xml
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/plotting/bar_chart.xml
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_binned_scores_in_intervals.xml
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into protect-release-branch
Commit: 9c4587969ec71a0759e9a46053ffaf13e98944da
https://github.com/galaxyproject/galaxy/commit/9c4587969ec71a0759e9a46053ff…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
typo spotted by @nsoranzo
Commit: d62824892ccfbdd20b5ff6af46b8af61eca3c8b9
https://github.com/galaxyproject/galaxy/commit/d62824892ccfbdd20b5ff6af46b8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Merge pull request #3562 from martenson/protect-release-branch
add a task to protect the release branch in github
Compare: https://github.com/galaxyproject/galaxy/compare/c952f1be3360...d62824892ccf
1
0
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: f9edf39f58b9942b461e5238c9df60ab5765faea
https://github.com/galaxyproject/galaxy/commit/f9edf39f58b9942b461e5238c9df…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
Migrate galaxy_utils to a wheel.
Alternative approach to #3542 which was not future proof with Conda dependencies. I think this should be now.
xref #3364 #2994 http://dev.list.galaxyproject.org/Tools-using-Galaxy-s-Python-library-td467…
Rebased with fixes from @nsoranzo and @mvdbeek.
Commit: 16a97e47c70f544d7acd30aac107a6687f01b736
https://github.com/galaxyproject/galaxy/commit/16a97e47c70f544d7acd30aac107…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-05 (Sun, 05 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
Merge pull request #3551 from jmchilton/galaxy_utils_external
[17.01] Migrate galaxy_utils to a wheel.
Compare: https://github.com/galaxyproject/galaxy/compare/43873b8a6de5...16a97e47c70f
1
0
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
1
0
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
1
0
[galaxyproject/galaxy] f985b6: Fix new history naming for batchmode workflow runs
by GitHub 04 Feb '17
by GitHub 04 Feb '17
04 Feb '17
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: f985b613ea1002a6595e073dfb459880ad7fdfdf
https://github.com/galaxyproject/galaxy/commit/f985b613ea1002a6595e073dfb45…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
Log Message:
-----------
Fix new history naming for batchmode workflow runs
Commit: 4df803a930c1546d41e4adeef9a0cc286cf6ada0
https://github.com/galaxyproject/galaxy/commit/4df803a930c1546d41e4adeef9a0…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
Log Message:
-----------
Merge pull request #3532 from guerler/fix_new_history_naming
[16.10] Fix new history naming for batchmode workflow runs
Commit: 934bf6b056bc2475b217d62524e95de564c7a7a8
https://github.com/galaxyproject/galaxy/commit/934bf6b056bc2475b217d62524e9…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Ensure toolbox conf watcher updates cached hash when config change is
detected
Commit: b41b8e305bac3425b9bd20cda43936b23bd02abd
https://github.com/galaxyproject/galaxy/commit/b41b8e305bac3425b9bd20cda439…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Merge pull request #3558 from natefoo/toolconf-watch-hash
[16.10] Ensure toolbox conf watcher updates cached hash when config change is detected
Commit: 43873b8a6de5a6f1669f8364fff54c206b5f2f84
https://github.com/galaxyproject/galaxy/commit/43873b8a6de5a6f1669f8364fff5…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Merge pull request #3560 from galaxyproject/release_16.10
[17.01] Merge 16.10 into 17.01
Compare: https://github.com/galaxyproject/galaxy/compare/49970e786fcf...43873b8a6de5
1
0