Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 51c586c264f2acd912060297804d61c2539f2483
https://github.com/galaxyproject/galaxy/commit/51c586c264f2acd912060297804d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix tools placed outside of panel section
Occasionally tools were being installed outside of the selected too panel
section. In the log one would find contradicting messages such as
```
tool_shed.util.repository_util DEBUG 2016-11-04 11:06:17,854 Adding new row for repository 'sra_tools' in the tool_shed_repository table, status set to 'New'.
galaxy.tools.toolbox.base DEBUG 2016-11-04 11:06:17,886 Appending to tool panel section: NCBI SRA Tools
172.17.0.1 - - [04/Nov/2016:11:06:15 +0000] "POST
/admin_toolshed/prepare_for_install HTTP/1.1" 200 -
"http://localhost/admin_toolshed/prepare_for_install?changeset_revisions=62e…"
"
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/54.0.2840.71 Safari/537.36
nvalid tool_panel_section_key "ncbi_sra_tools" specified. Tools will be
loaded outside of sections in the tool panel.
```
The intermittent POST is picked up by a different thread, that didn't
have its toolbox updated with the new section.
To circumvent this, we send the `create_panel_section` task to all
threads.
Commit: 4365b907293e366d4ad48396bb5c9dc00f134611
https://github.com/galaxyproject/galaxy/commit/4365b907293e366d4ad48396bb5c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Fix toolbox unittests
Commit: 202f96c73114fe9f05ed295505243ba17716b0e2
https://github.com/galaxyproject/galaxy/commit/202f96c73114fe9f05ed29550524…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-06 (Sun, 06 Nov 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Merge pull request #3125 from mvdbeek/fix_invalid_section_key
Fix tools placed outside of panel section
Compare: https://github.com/galaxyproject/galaxy/compare/58b7b6cf15c5...202f96c73114
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2956f94aa06f62fc0adde93d5aacc69e693a62d8
https://github.com/galaxyproject/galaxy/commit/2956f94aa06f62fc0adde93d5aac…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
Log Message:
-----------
BLAST database *.loc.sample files
Commit: 2e36fdb0bd0fff246eeff6322542c31150804eb2
https://github.com/galaxyproject/galaxy/commit/2e36fdb0bd0fff246eeff6322542…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M config/tool_data_table_conf.xml.sample
Log Message:
-----------
Include all three BLAST .loc files in data table conf
Commit: f060795335e564f79ed3f28b5390db4ac8e7d735
https://github.com/galaxyproject/galaxy/commit/f060795335e564f79ed3f28b5390…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
A lib/galaxy/datatypes/blast.py
Log Message:
-----------
BLAST datatypes as of standalone blast_datatypes v0.0.21
Copied from separate BLAST+ Galaxy repository,
https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatyp…
Currently available from the Galaxy Tool Shed,
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
Primary contributors to the BLAST datatypes for Galaxy:
* Peter Cock (The James Hutton Institute, UK)
* Edward Kirton
* Nicola Soranzo
* Bjoern Gruening
This work and the associated BLAST+ wrappers can be cited as:
NCBI BLAST+ integrated into Galaxy.
P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
*GigaScience* 2015, 4:39
DOI: http://dx.doi.org/10.1186/s13742-015-0080-7
Commit: a53e9fa9dbd635ee6359fb6b68371a3d0e5159c6
https://github.com/galaxyproject/galaxy/commit/a53e9fa9dbd635ee6359fb6b6837…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Remove unused imports
Commit: bdd046a2e86c935e1c932421a25e7ed480aacdf8
https://github.com/galaxyproject/galaxy/commit/bdd046a2e86c935e1c932421a25e…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Missing import required for use as doctest
Commit: 193651c88d325a5c1710def37386524e956ac147
https://github.com/galaxyproject/galaxy/commit/193651c88d325a5c1710def37386…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
Log Message:
-----------
Sample blastxml file for sniff doctest
Commit: ea717dd0013c9ef69d5ea0cd8edb72f44546e5d8
https://github.com/galaxyproject/galaxy/commit/ea717dd0013c9ef69d5ea0cd8edb…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Add BLAST datatypes to datatypes_conf.xml.sample
Commit: 8b73de6f50572ea2fb815fa75460f5850b877f12
https://github.com/galaxyproject/galaxy/commit/8b73de6f50572ea2fb815fa75460…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Adjust import order as per Galaxy tox flake8 checks
Commit: f9eff95613cdf27f5300ea393418f017da8e8012
https://github.com/galaxyproject/galaxy/commit/f9eff95613cdf27f5300ea393418…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
More accurate module docstring
Commit: 0152254a6f455bae538c96f3ce85baee1ae1c9f8
https://github.com/galaxyproject/galaxy/commit/0152254a6f455bae538c96f3ce85…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/sniff.py
Log Message:
-----------
megablast_xml_parser_test1.blastxml should now sniff as blastxml
Commit: 48664fa2fe7f43ee667e9fa4ece51852632570e7
https://github.com/galaxyproject/galaxy/commit/48664fa2fe7f43ee667e9fa4ece5…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Ensure all BLAST datatype contributors in CONTRIBUTORS.md
Commit: ce5ceeb29b134a84cf577f0bf2244011ac0cdfe4
https://github.com/galaxyproject/galaxy/commit/ce5ceeb29b134a84cf577f0bf224…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Give my work email address as well.
My Galaxy work to date has been while employed at
The James Hutton Institute (UK).
Commit: 17783cec36f4bf0d3b79137842dad52a64f80da2
https://github.com/galaxyproject/galaxy/commit/17783cec36f4bf0d3b79137842da…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
Log Message:
-----------
Tweak testing installing BLAST datatypes from Tool Shed
This is a short term pragmatic solution for the planned return
of the BLAST datatypes to the main Galaxy distribution. Long
term an additional test using an alternative Tool Shed defined
datatype may be needed.
Commit: 7fe47735209e43501e6116453a2fd961e5934429
https://github.com/galaxyproject/galaxy/commit/7fe47735209e43501e6116453a2f…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Clearer error message if BLAST XML header too long
Commit: 4159770ed9d173a2a3b45f7615aa764be9e99188
https://github.com/galaxyproject/galaxy/commit/4159770ed9d173a2a3b45f7615aa…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Explicitly label blast.py as MIT licensed.
Edward Kirton's contributions were made under the MIT license
while this code was developed outside of the main Galaxy
Project and distributed via the Galaxy Tool Shed). We have not
been able to contact him to authorise re-licensing under the
main Galaxy Project's license instead.
Commit: b5ba9605e56b8a8c8a827c6bd83208314ab8ccf0
https://github.com/galaxyproject/galaxy/commit/b5ba9605e56b8a8c8a827c6bd832…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Mark BLAST XML with EDAM ontology terms.
As per Herve Menager, EDAM format should be 3331 and data 0857
(sequence search results).
Commit: 58b7b6cf15c57a9a42340baeb2131e42cc76d02d
https://github.com/galaxyproject/galaxy/commit/58b7b6cf15c57a9a42340baeb213…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-05 (Sat, 05 Nov 2016)
Changed paths:
M CONTRIBUTORS.md
M config/datatypes_conf.xml.sample
M config/tool_data_table_conf.xml.sample
A lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
Log Message:
-----------
Merge pull request #2696 from peterjc/blast_datatypes
Returning Blast datatypes to Galaxy core (work-in-progress)
Compare: https://github.com/galaxyproject/galaxy/compare/b1892b7e30f9...58b7b6cf15c5
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 66dec1d580b426ad955db03608ec7da7eb5c5018
https://github.com/galaxyproject/galaxy/commit/66dec1d580b426ad955db03608ec…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M test/base/driver_util.py
Log Message:
-----------
Add download_to_file function to galaxy.util
Use it in 2 places:
- test/base/driver_util.py (thus adding timeout and chunking)
- lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
where the total download timeout is substituted with the usual
urllib timeout
Commit: b1892b7e30f9e2a9be94bd8ee064c0f548525bfe
https://github.com/galaxyproject/galaxy/commit/b1892b7e30f9e2a9be94bd8ee064…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M test/base/driver_util.py
Log Message:
-----------
Merge pull request #3100 from nsoranzo/followup_on_3013
Add download_to_file function to galaxy.util
Compare: https://github.com/galaxyproject/galaxy/compare/37399049552d...b1892b7e30f9