Nate Coraor
c893afda00
Merge branch 'dev' into smash_eggs
2015-10-19 11:46:58 -04:00
Nate Coraor
d92787557a
Move vvers and vurl vars to a more relevant scope.
2015-10-15 11:00:50 -04:00
Nate Coraor
433b79de2b
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs
2015-10-13 16:54:18 -04:00
Dannon Baker
b77496ec63
Update other quota manipulations to use the new user.adjust_quota_usage function.
2015-10-13 13:53:15 -04:00
Nate Coraor
744835bbfe
Allow the use of common_startup.sh's --skip-eggs from run_tests.sh, and
...
have tox pass this flag (so that dependencies are installed in the tox
envs)
2015-10-13 12:47:01 -04:00
Nate Coraor
665c4c299d
Handle the case where there are no conditional (heh) requirements
2015-10-01 15:38:58 -04:00
Dannon Baker
7f3ee5b167
Merge pull request #612 from lparsons/manual_builds
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Move manual_builds.txt to manual_builds.txt.sample
2015-09-24 17:10:49 -04:00
Nate Coraor
a44b2c2170
Rename galaxy.wheels to the more generalized galaxy.dependencies (since
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technically we don't care whether they are wheels), handle optional deps
more correctly. Add error handling to common_startup.sh.
2015-09-22 12:54:03 -04:00
Nate Coraor
93410ecf25
Fix additional lint errors created by modifying stuff in scripts/
2015-09-21 16:01:22 -04:00
Nate Coraor
0469ed29e0
Remove egg cruft from scripts/
2015-09-21 15:55:07 -04:00
Nate Coraor
97ad53f570
Merge remote-tracking branch 'upstream/dev' into smash_eggs
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Conflicts:
eggs.ini
lib/galaxy/__init__.py
lib/galaxy/datatypes/binary.py
lib/galaxy/datatypes/converters/bgzip.py
lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
lib/galaxy/datatypes/converters/interval_to_bed_converter.py
lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
lib/galaxy/datatypes/converters/interval_to_coverage.py
lib/galaxy/datatypes/converters/interval_to_fli.py
lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
lib/galaxy/datatypes/converters/maf_to_interval_converter.py
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
lib/galaxy/datatypes/coverage.py
lib/galaxy/eggs/__init__.py
lib/galaxy/eggs/dist.py
lib/galaxy/eggs/scramble.py
lib/galaxy/exceptions/__init__.py
lib/galaxy/jobs/runners/pbs.py
lib/galaxy/jobs/transfer_manager.py
lib/galaxy/model/__init__.py
lib/galaxy/model/migrate/check.py
lib/galaxy/model/orm/__init__.py
lib/galaxy/model/tool_shed_install/migrate/check.py
lib/galaxy/web/framework/__init__.py
lib/galaxy/web/framework/helpers/__init__.py
lib/galaxy/web/framework/middleware/sentry.py
lib/galaxy/web/framework/openid_manager.py
lib/galaxy/web/framework/webapp.py
lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
lib/galaxy/webapps/galaxy/controllers/dataset.py
lib/galaxy/webapps/galaxy/controllers/library_common.py
lib/galaxy/webapps/reports/controllers/workflows.py
lib/galaxy/webapps/tool_shed/controllers/repository.py
lib/galaxy/webapps/tool_shed/search/repo_search.py
lib/galaxy/webapps/tool_shed/search/tool_search.py
lib/galaxy_ext/metadata/set_metadata.py
lib/pulsar/client/config_util.py
lib/tool_shed/galaxy_install/install_manager.py
lib/tool_shed/galaxy_install/migrate/check.py
lib/tool_shed/grids/admin_grids.py
lib/tool_shed/grids/repository_grids.py
lib/tool_shed/repository_types/repository_suite_definition.py
lib/tool_shed/repository_types/tool_dependency_definition.py
lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
lib/tool_shed/scripts/check_repositories_for_functional_tests.py
lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
lib/tool_shed/util/basic_util.py
lib/tool_shed/util/encoding_util.py
lib/tool_shed/util/hg_util.py
scripts/check_eggs.py
scripts/dist-scramble.py
scripts/fetch_eggs.py
scripts/make_egg_packager.py
scripts/scramble.py
scripts/scramble/lib/scramble_lib.py
scripts/scramble/scripts/DRMAA_python-macosx.py
scripts/scramble/scripts/DRMAA_python-solaris.py
scripts/scramble/scripts/DRMAA_python.py
scripts/scramble/scripts/MySQL_python-solaris.py
scripts/scramble/scripts/MySQL_python.py
scripts/scramble/scripts/PyRods.py
scripts/scramble/scripts/bx_python-solaris.py
scripts/scramble/scripts/generic.py
scripts/scramble/scripts/pbs_python.py
scripts/scramble/scripts/psycopg2-linux.py
scripts/scramble/scripts/psycopg2-macosx.py
scripts/scramble/scripts/psycopg2-solaris.py
scripts/scramble/scripts/psycopg2.py
scripts/scramble/scripts/pysam-solaris.py
scripts/scramble/scripts/pysqlite.py
scripts/test_dist_egg.py
2015-09-21 15:02:47 -04:00
Nate Coraor
40bde6e102
Install required dependencies from requirements.txt rather than
...
convoluted galaxy.wheels method. Not sure why I was doing that.
Hackathons are dangerous places.
2015-09-21 13:21:13 -04:00
Nate Coraor
150c17b9e8
Do not explicitly require pexpect. If anyone wants to use the old and
...
mostly unused features that depend on it (namely remote sequencer
transfers via scp) they can pip install pexpect.
2015-09-17 13:56:44 -04:00
John Chilton
bd55650f06
Add testing environment variable GALAXY_TEST_LOGGING_CONFIG.
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Unifies logging through the testing process. Requires adding a Galaxy option to disable its own attempts to configure a different root logger.
2015-09-16 16:24:53 +01:00
Nicola Soranzo
cd456e186d
Print to stderr when calling sys.exit(1)
2015-09-11 19:05:37 +01:00
Nicola Soranzo
2625bc4bc0
Fix flake8 broken when merging 041c94bf78 from release_15.07 .
2015-09-02 16:30:50 +01:00
Nicola Soranzo
bcbeb75a68
Merge branch 'master' into dev
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Conflicts:
lib/tool_shed/dependencies/tool/tag_attribute_handler.py
2015-09-02 16:10:03 +01:00
John Chilton
4a05c07aa5
Fixup end of release items for release notes.
2015-08-27 13:04:17 +01:00
John Chilton
041c94bf78
Release notes for 15.07.
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This includes a script to boot strap the notes for future releases, updated announcement page for 15.07, and new announcement page for 15.10.
2015-08-27 12:00:18 +01:00
Nicola Soranzo
0f883ef776
Merge branch 'release_15.07' into dev
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Conflicts:
lib/galaxy/model/__init__.py
2015-08-20 14:12:27 +01:00
Nicola Soranzo
a34f13a9f6
Merge branch 'release_15.05' into release_15.07
2015-08-20 14:07:09 +01:00
Nicola Soranzo
238d908cce
Fix purging datasets whose total_size is None.
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Fix the error:
Removing disk, file /opt/galaxy/database/files/000/dataset_192.dat
Error attempting to purge data file: /opt/galaxy/database/files/000/dataset_192.dat error: unsupported operand type(s) for -=: 'Decimal' and 'NoneType'
when running:
python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 10 -3 -r
2015-08-19 15:33:54 +01:00
Lance Parsons
5810a853b0
Move manual_builds.txt to manual_builds.txt.sample to allow for customization
2015-08-18 14:00:30 -04:00
Martin Cech
7a39867933
Merge branch 'release_15.07' into dev
2015-08-06 11:29:18 -04:00
Martin Cech
4d697b7b50
fix overriding the name variable
2015-08-06 10:38:12 -04:00
Martin Cech
871e253015
merge 15.07 into dev
2015-08-06 09:33:44 -04:00
Martin Cech
d583c376a5
flake8 spotted by @nsoranzo
2015-08-05 14:27:25 -04:00
Martin Cech
0ad5c8a1a8
fix TS search index building script to properly visit subdirectories
2015-08-05 13:55:01 -04:00
Dannon Baker
c18887c0d1
Clean up pam auth helper.
2015-07-17 08:06:04 -04:00
Dannon Baker
7019e32305
Merge with dev
2015-07-17 07:54:25 -04:00
Nate Coraor
cb8f6354de
Merge pull request #458 from pvanheus/auth_pam
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AuthProvider for PAM (Pluggable Authentication Modules)
2015-07-14 22:12:17 -04:00
Peter van Heusden
b9c9f11ce1
* New PAM AuthProvider for interfacing with the Pluggable Authentication Module system ( http://www.linux-pam.org/ )
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* Helper script to allow authenticating against modules as root
2015-07-15 00:47:13 +02:00
Nicola Soranzo
cc9b0bed85
Fix all E712 errors. Standardize sqlalchemy imports.
2015-07-14 20:49:34 +01:00
Nicola Soranzo
34d9388456
Use os.pardir everywhere instead of '..' .
2015-07-14 16:20:29 +01:00
Nicola Soranzo
6569c2dcc3
Partially lint scripts/ .
2015-07-13 20:13:28 +01:00
Nate Coraor
5501917346
Install modified pip in develop/edit mode so it won't be reinstalled
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every time (courtesy @jxtx).
2015-07-05 10:50:54 -04:00
Nate Coraor
a24134c447
Install modified pip for fetching Linux wheels, fetch wheels from
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wheels.galaxyproject.org
2015-07-05 05:24:15 -04:00
Nate Coraor
633061f3e0
WIP: Stop using eggs, start using prebuilt wheels.
2015-07-04 15:18:50 -04:00
Martin Cech
eb54b1d854
expose searching full TS toolset over a separate index
...
the index is created by the same script (build_ts_whoosh_index.py)
2015-06-19 16:24:27 -04:00
John Chilton
4e82c80293
Fix for 38679a0d32.
...
Reported by @golharam.
2015-06-18 15:57:49 -04:00
Martin Cech
508b685c70
fix common API scripts so they dont fail when response has no url param
2015-06-15 16:12:21 -04:00
John Chilton
374795f631
Only cleanup successful jobs when testing.
...
As per the recommendation of Ryan G. at http://dev.list.galaxyproject.org/keep-job-output-and-scripts-on-failed-tests-td4667327.html .
I considered making this 'never' - since those files will get cleaned up at the end anyway. This would actually reduce our test coverage related to job cleanup logic - so I have decided this is a fine a middle ground.
2015-06-15 09:53:59 -04:00
John Chilton
584f673f8d
Merge remote-tracking branch 'jmchilton/dev' into ts-search-expansion
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Conflicts:
lib/galaxy/webapps/tool_shed/buildapp.py
2015-06-15 09:43:59 -04:00
John Chilton
732abcc0db
Merge remote-tracking branch 'jmchilton/release_15.05' into dev
2015-06-08 14:04:28 -04:00
Nicola Soranzo
292d16a593
Mark also HDAs as purged when purging datasets via cleanup script.
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This will make purged datasets be shown as purged in histories,
preventing them to be undeleted through the UI.
This will not fix datasets previously purged through this script,
scripts/cleanup_datasets/pgcleanup.py may be used for that.
2015-06-04 18:06:01 +01:00
Dannon Baker
e56b2a3433
Merge pull request #274 from dpryan79/dev
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Add usage information to python cleanup scripts
2015-06-02 07:57:02 -04:00
John Chilton
3946ff50bb
Merge pull request #80 from erasche/jbrowse-ie
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Add EDAM IDs to datatypes
2015-05-22 09:42:59 -05:00
dpryan79
00eb96923f
Add a missing period in populate_uuid.py
2015-05-20 13:01:40 +02:00
dpryan79
0ff5a050d5
Indentation fix
2015-05-19 21:55:36 +02:00
dpryan79
0763cab37a
Update the remainder of the python cleanup scripts
2015-05-19 21:53:45 +02:00
Nate Coraor