galaxy-commits October 2016

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[galaxyproject/galaxy] 83a294: Lint fixes to workflow controller
by GitHub 27 Oct '16

27 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83a29454caea72915386c58a7188e08cd4597d35 https://github.com/galaxyproject/galaxy/commit/83a29454caea72915386c58a7188… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Lint fixes to workflow controller Commit: 660d70f8b4da32f5ebd5981ad9eb27e87a79da73 https://github.com/galaxyproject/galaxy/commit/660d70f8b4da32f5ebd5981ad9eb… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #3103 from dannon/minor_style_fixes Lint fixes to workflow controller Compare: https://github.com/galaxyproject/galaxy/compare/0eff2ec6479b...660d70f8b4da

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[galaxyproject/galaxy] 1288cf: Add workflow save-as functionality. Issue 3000
by GitHub 27 Oct '16

27 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1288cf0505eea6139bf9f34d60e6b255268d717d https://github.com/galaxyproject/galaxy/commit/1288cf0505eea6139bf9f34d60e6… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Add workflow save-as functionality. Issue 3000 Commit: 2ab0b18706dc54cde3507e194a935f513c68119c https://github.com/galaxyproject/galaxy/commit/2ab0b18706dc54cde3507e194a93… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Allow names with spaces Commit: 38464b5b284289c66263adc19afa0a6be2e24389 https://github.com/galaxyproject/galaxy/commit/38464b5b284289c66263adc19afa… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Originating workflow must be unchanged, load save as workflow to editor on save. Commit: 0eff2ec6479b321d9fc653aa9eaf79559fc50e56 https://github.com/galaxyproject/galaxy/commit/0eff2ec6479b321d9fc653aa9eaf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge remote-tracking branch 'tmcgowan/issue_3000' into dev Compare: https://github.com/galaxyproject/galaxy/compare/541643d7fe28...0eff2ec6479b

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[galaxyproject/infrastructure-playbook] 9db378: Increase upstream proxy timeout for galaxy install...
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9db37851eff6bc685efa1be40b6601a5257ca2ed https://github.com/galaxyproject/infrastructure-playbook/commit/9db37851eff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M taccenv/host_vars/galaxy04.tacc.utexas.edu.yml Log Message: ----------- Increase upstream proxy timeout for galaxy installers

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[galaxyproject/galaxy] 69636f: Add CEL file as a datatype
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69636f5e65e6b3ad2c8d7e3c300cd81418bb6206 https://github.com/galaxyproject/galaxy/commit/69636f5e65e6b3ad2c8d7e3c300c… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add CEL file as a datatype Commit: 7e2725d1250fef33d1d03cc4e15b29de6f1a540f https://github.com/galaxyproject/galaxy/commit/7e2725d1250fef33d1d03cc4e15b… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add CEL datatypes to datatypes conf sample Commit: f891034390908bd6a374bf140a57ac76afefefd9 https://github.com/galaxyproject/galaxy/commit/f891034390908bd6a374bf140a57… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Lowercase the datatypes, add edam_data, thanks @nsoranzo Commit: a6f1783b366293a0d87ee941882e449f092cce95 https://github.com/galaxyproject/galaxy/commit/a6f1783b366293a0d87ee941882e… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: A lib/galaxy/datatypes/test/test.CEL Log Message: ----------- Small test case CEL datatype, v4 Commit: 827e61a98cdfb3074d49df25b3ac0b30ce32d0bc https://github.com/galaxyproject/galaxy/commit/827e61a98cdfb3074d49df25b3ac… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add doctests Commit: 5c1d0982e33e3c5464bb6374d33ed9a7bb76a648 https://github.com/galaxyproject/galaxy/commit/5c1d0982e33e3c5464bb6374d33e… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- lint issues Commit: 541643d7fe28abeac4a69147aa3ae30f84d438ae https://github.com/galaxyproject/galaxy/commit/541643d7fe28abeac4a69147aa3a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.CEL Log Message: ----------- Merge pull request #3073 from nturaga/add_cel_datatype Add CEL datatype Compare: https://github.com/galaxyproject/galaxy/compare/f21279d473fa...541643d7fe28

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[galaxyproject/usegalaxy-playbook] 1d8cc9: Fix admin users
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1d8cc9c82c9ed83814d8b5d46780634e29a70571 https://github.com/galaxyproject/usegalaxy-playbook/commit/1d8cc9c82c9ed838… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M production/secret_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Fix admin users

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[galaxyproject/galaxy] 2ec9c0: Log loading of resources from *.loc files
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ec9c05380356ba543b29bae44cc3bdd947196a2 https://github.com/galaxyproject/galaxy/commit/2ec9c05380356ba543b29bae44cc… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Log loading of resources from *.loc files Example output: ``` $ grep "lines from" paster.log galaxy.tools.data DEBUG 2016-10-26 10:24:22,742 Loaded 0 lines from 'tool-data/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2016-10-26 10:24:22,753 Loaded 0 lines from 'tool-data/bfast_indexes.loc' for 'bfast_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,848 Loaded 24 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2016-10-26 10:24:22,859 Loaded 0 lines from 'tool-data/maf_index.loc' for 'indexed_maf_files' galaxy.tools.data DEBUG 2016-10-26 10:24:22,865 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2016-10-26 10:24:22,878 Loaded 0 lines from 'tool-data/perm_base_index.loc' for 'perm_base_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,890 Loaded 0 lines from 'tool-data/perm_color_index.loc' for 'perm_color_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,895 Loaded 0 lines from 'tool-data/picard_index.loc' for 'picard_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,899 Loaded 0 lines from 'tool-data/picard_index.loc' for 'srma_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,937 Loaded 0 lines from 'tool-data/mosaik_index.loc' for 'mosaik_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,943 Loaded 0 lines from 'tool-data/twobit.loc' for 'twobit' ... galaxy.tools.data DEBUG 2016-10-26 10:24:24,036 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2016-10-26 10:24:24,106 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2016-10-26 10:24:24,112 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_d.loc' for 'blastdb_d' ``` Commit: f21279d473fa8f19d3881af35d3066e79d757304 https://github.com/galaxyproject/galaxy/commit/f21279d473fa8f19d3881af35d30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #3099 from peterjc/patch-5 Log loading of resources from *.loc files Compare: https://github.com/galaxyproject/galaxy/compare/90d143cda16d...f21279d473fa

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[galaxyproject/galaxy] fc0271: Fix BLAST database *.loc files inconsistency
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fc027124e73ee391e4b4045b2abc68fd942f910c https://github.com/galaxyproject/galaxy/commit/fc027124e73ee391e4b4045b2abc… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Fix BLAST database *.loc files inconsistency We should have all of the ``blast*.loc`` files in the sample configuration, or none of them. Historically Galaxy included only the nucleotide BLAST database ``blastdb.loc`` file for use with mega-blast, with ``blastdb_p.loc`` later for protein databases added as part of the BLAST+ suite (which initially was in the main Galaxy repository). In a3018feb028658fc3a7071803b7b49cb575e7358 the mega-blast tool was moved to the Tool Shed, and the ``blastdb.loc`` entry removed. Likewise the BLAST+ tools were moved to the Tool Shed, but the ``blastdb_p.loc`` entry remains. Later (on the Tool Shed only?) ``blastdb_d.loc``was added for protein domain databases. Commit: 90d143cda16d7c7a0938e255c08bf9db7fea727c https://github.com/galaxyproject/galaxy/commit/90d143cda16d7c7a0938e255c08b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Merge pull request #3098 from peterjc/patch-6 Fix BLAST database *.loc files inconsistency Compare: https://github.com/galaxyproject/galaxy/compare/ab42b7b15c50...90d143cda16d

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[galaxyproject/galaxy] ca8cd5: Avoid pointless lambda function
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca8cd524a1f882b7de2aaf5f56d8b2878c07739a https://github.com/galaxyproject/galaxy/commit/ca8cd524a1f882b7de2aaf5f56d8… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Avoid pointless lambda function The lambda function used a ternary if/else anyway, just do this directly - its shorter and clearer. Commit: ab42b7b15c50c7ae4a4a582ebc1df2780e1538de https://github.com/galaxyproject/galaxy/commit/ab42b7b15c50c7ae4a4a582ebc1d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #3097 from peterjc/patch-4 Avoid pointless lambda function Compare: https://github.com/galaxyproject/galaxy/compare/35346fdb3e67...ab42b7b15c50

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[galaxyproject/galaxy] 17da51: Include filenames in loc file DEBUG lines
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17da51abdc61e9fb1e3f76b36316c9dbf3c836e6 https://github.com/galaxyproject/galaxy/commit/17da51abdc61e9fb1e3f76b36316… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Include filenames in loc file DEBUG lines This will help debugging where multiple (possibly conflicting) ``*.loc`` files come from, e.g. ``` galaxy.tools.data DEBUG 2016-10-25 18:34:50,841 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2016-10-25 18:34:51,356 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2016-10-25 18:34:51,359 Loading another instance of data table 'blastdb_p', attempting to merge content. galaxy.tools.data DEBUG 2016-10-25 18:34:51,375 Loaded tool data table 'blastdb_d' ``` Evidently I may have at least two copies of ``blastdb_p.loc``, but where are they? Commit: 35346fdb3e6764b14ae3359fb9ea31c03d932ea0 https://github.com/galaxyproject/galaxy/commit/35346fdb3e6764b14ae3359fb9ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #3095 from peterjc/patch-4 Include filenames in loc file DEBUG lines Compare: https://github.com/galaxyproject/galaxy/compare/8da4ad6563f2...35346fdb3e67

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[galaxyproject/usegalaxy-playbook] 860a2d: Increase htseq-count memory to 16GB
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 860a2d104193a693a5f8f224c29a14df956d13d3 https://github.com/galaxyproject/usegalaxy-playbook/commit/860a2d104193a693… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase htseq-count memory to 16GB

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galaxy-commits October 2016