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Author SHA1 Message Date
Nate Coraor 7010e38b6f Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs 2015-10-27 17:07:28 -04:00
carlfeberhard 3529ef6b6e Merge pull request #995 from natefoo/smash-eggs-bugfix1 
binary_compatibility.py shouldn't fail
 2015-10-27 17:00:41 -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
carlfeberhard a71f504b1e Merge pull request #959 from martenson/track-newlibs 
add google analytics tracking to newlibs, propagate ga_code to JS config
 2015-10-27 16:30:42 -04:00
Martin Cech f0fbd25526 Merge branch 'dev' into track-newlibs 
Conflicts:
	static/maps/galaxy.library.js.map
	static/scripts/galaxy.library.js
 2015-10-27 16:30:05 -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
John Chilton e31ec7b0c8 Merge pull request #989 from natefoo/smash_eggs 
Add a script for creating binary-compatibility.cfg and run it from common_startup.sh
 2015-10-27 19:18:59 +00:00
Nate Coraor 6d7be0a218 Merge branch 'release_15.10' of https://github.com/galaxyproject/galaxy into dev 2015-10-27 15:11:14 -04:00
Nate Coraor 1a3a594d4e Allow CentOS to install RHEL wheels. 2015-10-26 15:47:51 -04:00
Nate Coraor 9503f1ddf3 Fix the raven conditional requirement 2015-10-26 15:36:54 -04:00
Daniel Blankenberg 5f3fbdefbe Merge pull request #988 from natefoo/smash_eggs 
Add a --dev-wheels arg to common_startup.sh
 2015-10-26 15:05:17 -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
Eric Rasche ef08ef4ead Merge pull request #986 from natefoo/smash_eggs 
Do not attempt to read the `load` attribute of job runner plugins that do not have a `load` attribute.
 2015-10-26 18:05:31 +00:00
Nate Coraor 7975798afb Do not attempt to read the load attribute of job runner plugins that 
do not have a `load` attribute.

`load` is an optional attrib on the <plugin> tag in job_conf.xml, used
by the dynamic runner (which is always/automatically loaded) to pass
plugin params. Galaxy servers using a `load`-less plugin will fail to
start if using run.sh without this fix.
 2015-10-26 11:41:11 -04:00
Dannon Baker e423ab6246 Merge pull request #428 from natefoo/smash_eggs 
Replace eggs with wheels
 2015-10-22 18:44:35 -04:00
Nate Coraor 88683c3c40 Unset $PYTHONPATH in run.sh and common_startup.sh unless --skip-env is 
provided.
 2015-10-22 18:42:06 -04:00
Aysam Guerler 112c0390d5 Merge pull request #971 from dannon/grid_batch_fixes 
Grid batch operation fixes
 2015-10-22 16:02:23 -04:00
Nate Coraor 737596413f Pass relevant args from run.sh to common_startup.sh. 2015-10-22 15:04:00 -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 0cbaf3b8c5 Use proper PEP-440 local version identifiers for modified dependencies. 2015-10-22 15:01:29 -04:00
Daniel Blankenberg eca98ec828 Merge pull request #856 from dannon/dynatree_upgrade 
Dynatree upgrade
 2015-10-22 14:31:15 -04:00
James Taylor 1c527d3784 Merge pull request #902 from dannon/issue_management 
New policies for bug and issue handling, and roadmap management.
 2015-10-22 14:29:27 -04:00
Dannon Baker dab1ce3f03 Merge pull request #973 from natefoo/composite-history-import-export 
[15.10] Fix for missing included files on history export and import
 2015-10-22 12:57:43 -04:00
Vimalkumar Velayudhan dfb59002ba Use object store for imported history datasets and included files 
(cherry picked from commit ea89dd8f14)
 2015-10-22 12:51:48 -04:00
Vimalkumar Velayudhan 57d0620292 Fix for missing included files on history export and import. 
Notes:

If a history was exported previously, galaxy would just serve the cached version.
In that case, it is better to make some changes to the history for example, by re-running
the last job and then exporting it.

Export of histories that haven't been exported previously should work without problems.

(cherry picked from commit 9ea0fee48a)
 2015-10-22 12:51:42 -04:00
Nate Coraor 53f924fbaf Merge pull request #417 from vimalkumarvelayudhan/dev 
Fix for missing included files on history export and import.
 2015-10-22 12:27:26 -04:00
Nate Coraor 7e372d3cd0 Updates to vis data providers for pysam API changes 2015-10-22 11:43:01 -04:00
Nate Coraor 048f0be1be Talked to Dan, who corrected me on a few things. Also, forgot that the 
whole reason we use a modified pysam is for the index_filename param...
 2015-10-22 11:23:20 -04:00
Nate Coraor af89922aee Update the BAM datatype for pysam API changes. index_file also no longer 
exists (the index must be filename + b".bai" or filename[:-4] + b".bai")
=/.  Removing it here is okay since the impact is that we can't fetch()
random regions or use .pileup(), neither of which are done here. But it
might be a problem for galaxy.visualization.data_providers.genome.
 2015-10-22 10:52:57 -04:00
John Chilton 3fe148dd19 Merge pull request #970 from guerler/fix_history_extract_001 
[15.10] Fix workflow extraction from history
 2015-10-22 15:50:23 +01:00
Daniel Blankenberg cbc87383db Merge pull request #969 from dannon/ie_explorations 
Fix base panels to include scripts as the last element of the body,
 2015-10-22 08:16:16 -04:00
Dannon Baker 82e96140a1 Merge pull request #967 from martenson/remove-reports-autorefresh 
[15.10] remove the autorefresh on Reports app homepage
 2015-10-22 08:11:55 -04:00
Dannon Baker 8716eefc9e Merge branch 'master' into dev 2015-10-21 18:16:44 -04:00
Dannon Baker ab7ec7b3ab Merge pull request #963 from blankenberg/gs_release_15.10 
[15.10] Set <options sanitize="False"> for genomespace_importer.xml
 2015-10-21 18:14:53 -04:00
Dannon Baker 6260bd1d0f Strip whitespace in grid-view.js 2015-10-21 17:55:40 -04:00
Dannon Baker c3db6af560 Fix grid batch operations. This should correctly display and request confirmation for batch operations (such as delete a set of <GalaxyObjects> which is scary without a confirmation). It also fixes it to where grid bulk operations actually work in IE. 2015-10-21 17:54:40 -04:00
guerler 8a0a445ec3 Fix workflow extraction from history 2015-10-21 17:36:44 -04:00
guerler 9d3893ed63 Undo commit, wrong branch 2015-10-21 17:26:33 -04:00
guerler ee327702d7 Fix workflow extraction from history 
Fix history extraction by returning value dictionary

Remove previous fix
 2015-10-21 17:20:42 -04:00
Dannon Baker a5814e8f3b Merge master-> dev. Resolved one conflict on style build. 2015-10-21 15:14:04 -04:00
John Chilton 0f0d14ae51 Merge pull request #960 from dannon/quick_fix 
S3ObjectStore followup fix
 2015-10-21 19:56:00 +01:00
Martin Cech f3bfa2f56b remove the autorefresh on Reports app 
because of how long each page takes on Main the request for a subpage
would timeout because new autorefresh request would be automatically
issued
 2015-10-21 14:22:41 -04:00
Eric Rasche 92666cdf66 Merge pull request #965 from dannon/login_req 
[15.10] Fix endless redirect cycle when login is required
 2015-10-21 12:02:50 -05:00
Dannon Baker 849458f37b Merge pull request #955 from common-workflow-language/yaml_select 
Improvements and fixes for abstract tool interface
 2015-10-21 12:43:32 -04:00
Dannon Baker 6f5aafe627 For require_login=True, redirect directly to login without showing empty (and broken) looking panels, and potentially hitting an endless reload cycle. 2015-10-21 12:19:00 -04:00
Daniel Blankenberg a02e0f19c8 Set <options sanitize="False"> for genomespace_importer.xml 2015-10-21 11:33:45 -04:00
Dannon Baker 15713c265f Remove historical config_xml. 2015-10-21 09:26:30 -04:00
Dannon Baker 320724a183 Merge pull request #853 from mr-c/storableobject 
doc updates for ObjectStore
 2015-10-21 08:47:58 -04:00
Michael R. Crusoe 4f0ec1eaf2 Merge pull request #1 from dannon/storableobject 
Revert most of the 79-char linewrapping in objectstore
 2015-10-21 15:10:24 +03:00
Nate Coraor 5098b7cb27 Downgrade twill to 0.9.1 so we don't have to install lxml, which won't 
compile because libxml-dev isn't installed in the testing image, so we'd
have to rebuild it yet again...
 2015-10-20 20:23:10 -04:00