Nate Coraor
7010e38b6f
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs
2015-10-27 17:07:28 -04:00
Nate Coraor
9563f121e8
binary_compatibility.py shouldn't fail on platforms that don't return
...
anything for get_specific_platform() (e.g. things other than Linux).
2015-10-27 16:41:27 -04:00
Nate Coraor
b7c8a6d334
Rename lib/galaxy/main.py to scripts/galaxy-main since that makes more
...
sense and doesn't result in lib/galaxy/ being added to sys.path.
Create a symlink at lib/galaxy/main.py for backward compatibility.
2015-10-27 16:03:33 -04:00
Nate Coraor
1a3a594d4e
Allow CentOS to install RHEL wheels.
2015-10-26 15:47:51 -04:00
Nate Coraor
d90ba82e92
Add a --dev-wheels arg to common_startup.sh (called by run_tests.sh by
...
default) that will install things in dev-requirements.txt.
2015-10-26 14:07:00 -04:00
Nate Coraor
88683c3c40
Unset $PYTHONPATH in run.sh and common_startup.sh unless --skip-env is
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provided.
2015-10-22 18:42:06 -04:00
Nate Coraor
4a5f5f44dc
Install our modified pip as a wheel from wheels.galaxyproject.org rather
...
than an editable directly from github.
Also, use `set -e` in scripts/common_startup.sh to fail if anything
fails, rather than chaining a bunch of things with `&&` but not properly
handling failure cases.
2015-10-22 15:02:14 -04:00
Nate Coraor
4a05d5ea12
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs
2015-10-20 18:59:06 -04:00
Nate Coraor
27ab6fe8f9
Use the database temp directory store the Mako template cache when
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running framework tests.
2015-10-20 13:56:28 -04:00
Nate Coraor
c893afda00
Merge branch 'dev' into smash_eggs
2015-10-19 11:46:58 -04:00
Eric Rasche
8a66701d4f
Don't re-upload if already there
2015-10-15 16:02:05 -05:00
Nate Coraor
d92787557a
Move vvers and vurl vars to a more relevant scope.
2015-10-15 11:00:50 -04:00
Eric Rasche
2cca823a78
Prepopulate memoization cache
2015-10-14 16:05:44 -05:00
Eric Rasche
6be301ca8a
Support local/non local data and paths including root
2015-10-14 15:02:27 -05:00
Eric Rasche
33925747b8
Allow linking only
2015-10-14 14:50:35 -05:00
Eric Rasche
aec9961407
Strip newlines
2015-10-14 14:43:08 -05:00
Eric Rasche
decca0e96a
Refactor to accept output of find
2015-10-14 14:37:21 -05:00
Eric Rasche
61f1cdf5d7
Added script to upload a directory to a data library
2015-10-14 14:16:45 -05:00
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
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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
...
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
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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
...
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
Nate Coraor