Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2956f94aa06f62fc0adde93d5aacc69e693a62d8 https://github.com/galaxyproject/galaxy/commit/2956f94aa06f62fc0adde93d5aacc... Author: peterjc <p.j.a.cock@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/2e36fdb0bd0fff246eeff6322542c... Author: peterjc <p.j.a.cock@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/f060795335e564f79ed3f28b5390d... Author: peterjc <p.j.a.cock@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_datatype... 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/a53e9fa9dbd635ee6359fb6b68371... Author: peterjc <p.j.a.cock@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/bdd046a2e86c935e1c932421a25e7... Author: peterjc <p.j.a.cock@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/193651c88d325a5c1710def373865... Author: peterjc <p.j.a.cock@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/ea717dd0013c9ef69d5ea0cd8edb7... Author: peterjc <p.j.a.cock@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/8b73de6f50572ea2fb815fa75460f... Author: peterjc <p.j.a.cock@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/f9eff95613cdf27f5300ea393418f... Author: peterjc <p.j.a.cock@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/0152254a6f455bae538c96f3ce85b... Author: peterjc <p.j.a.cock@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/48664fa2fe7f43ee667e9fa4ece51... Author: peterjc <p.j.a.cock@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/ce5ceeb29b134a84cf577f0bf2244... Author: peterjc <p.j.a.cock@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/17783cec36f4bf0d3b79137842dad... Author: peterjc <p.j.a.cock@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/7fe47735209e43501e6116453a2fd... Author: peterjc <p.j.a.cock@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/4159770ed9d173a2a3b45f7615aa7... Author: peterjc <p.j.a.cock@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/b5ba9605e56b8a8c8a827c6bd8320... Author: peterjc <p.j.a.cock@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/58b7b6cf15c57a9a42340baeb2131... Author: Björn Grüning <bjoern@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