December 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] bb8a5a: [16.10] Revert commands.shell changes from galaxyp...
by GitHub 14 Dec '16

14 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb8a5a2215c2fce0e1c5fb69f4665358d72905f6 https://github.com/galaxyproject/galaxy/commit/bb8a5a2215c2fce0e1c5fb69f466… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. It seems like people prefer to see the interactive shell https://github.com/galaxyproject/galaxy/issues/3259. See follow up here https://github.com/galaxyproject/galaxy/issues/3309. This also fixes an issue caused by the change of the constructor interface for CommandLineException in galaxyproject/galaxy#3129. Commit: 329108f81021e779db43a6a5c3b2808fd6c14b42 https://github.com/galaxyproject/galaxy/commit/329108f81021e779db43a6a5c3b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Merge pull request #3310 from jmchilton/shell_fix [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. Commit: da784093b3683b3586075aed3c70e38c3adc7c22 https://github.com/galaxyproject/galaxy/commit/da784093b3683b3586075aed3c70… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c4069da74292...da784093b368

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[galaxyproject/galaxy] bb4e7c: Add change_password functionality back to the user...
by GitHub 14 Dec '16

14 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb4e7c1a64df3b3c7c5c5c6391310883726a0af4 https://github.com/galaxyproject/galaxy/commit/bb4e7c1a64df3b3c7c5c5c639131… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Add change_password functionality back to the user controller. This was removed a bit too soon in https://github.com/galaxyproject/galaxy/commit/14e635aaee2699cb395443d802de…, without a replacement available. There's significant work involved in a replacement, so @guerler and I agreed to simply add the endpoint back for now. Commit: c4069da7429242bdbf7fb02da9716e4e8413512c https://github.com/galaxyproject/galaxy/commit/c4069da7429242bdbf7fb02da971… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3313 from dannon/password_reset_fixes Add change_password functionality back to the user controller. Compare: https://github.com/galaxyproject/galaxy/compare/e627f55be69a...c4069da74292

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[galaxyproject/galaxy] bb8a5a: [16.10] Revert commands.shell changes from galaxyp...
by GitHub 14 Dec '16

14 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: bb8a5a2215c2fce0e1c5fb69f4665358d72905f6 https://github.com/galaxyproject/galaxy/commit/bb8a5a2215c2fce0e1c5fb69f466… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. It seems like people prefer to see the interactive shell https://github.com/galaxyproject/galaxy/issues/3259. See follow up here https://github.com/galaxyproject/galaxy/issues/3309. This also fixes an issue caused by the change of the constructor interface for CommandLineException in galaxyproject/galaxy#3129. Commit: 329108f81021e779db43a6a5c3b2808fd6c14b42 https://github.com/galaxyproject/galaxy/commit/329108f81021e779db43a6a5c3b2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Merge pull request #3310 from jmchilton/shell_fix [16.10] Revert commands.shell changes from galaxyproject/galaxy#3129. Compare: https://github.com/galaxyproject/galaxy/compare/2c833499b130...329108f81021

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[galaxyproject/galaxy] b31c3b: Fix logo image when serving Galaxy from a subdirec...
by GitHub 14 Dec '16

14 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b31c3b24ac82a52d095a6e808c3e489dc308c045 https://github.com/galaxyproject/galaxy/commit/b31c3b24ac82a52d095a6e808c3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Fix logo image when serving Galaxy from a subdirectory. Commit: e627f55be69aead2c8aec7dfe7f230c125cf2f7d https://github.com/galaxyproject/galaxy/commit/e627f55be69aead2c8aec7dfe7f2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #3283 from jmchilton/logo_source Fix logo image when serving Galaxy from a subdirectory. Compare: https://github.com/galaxyproject/galaxy/compare/cf7119c474e2...e627f55be69a

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[galaxyproject/galaxy] 81a0cb: Update datatype converter tools
by GitHub 13 Dec '16

13 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 81a0cbf4721d7279e3a5b901e1646380d797635b https://github.com/galaxyproject/galaxy/commit/81a0cbf4721d7279e3a5b901e164… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml Log Message: ----------- Update datatype converter tools - dos2unix - Fix indentation - Add missing tool version - Remove deprecated <page> elements - Remove deprecated 'interpreter' attribute of <command> - Quote some data parameters in <command> - Remove some duplicated requirement Commit: ac8450f013284bc5b8502cfec0d64e809390ce02 https://github.com/galaxyproject/galaxy/commit/ac8450f013284bc5b8502cfec0d6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml Log Message: ----------- Add CDATA. Use && to concatenate commands. Quote $chromInfo Commit: cf7119c474e294eae79320fa5a51e5cdb5fa5835 https://github.com/galaxyproject/galaxy/commit/cf7119c474e294eae79320fa5a51… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml Log Message: ----------- Merge pull request #3305 from nsoranzo/converter_tools Update datatype converter tools Compare: https://github.com/galaxyproject/galaxy/compare/ad8d48c0a39d...cf7119c474e2

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[galaxyproject/galaxy] 8519e1: change conda channel order
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8519e12a474ec5337036136e19c66ed9352ac91a https://github.com/galaxyproject/galaxy/commit/8519e12a474ec5337036136e19c6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- change conda channel order Commit: 1f221aab22f4840d18847859f5099d4dc721b864 https://github.com/galaxyproject/galaxy/commit/1f221aab22f4840d18847859f509… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- change channel order Commit: 0c91f65a99c43608faaa9f7b504646a326d6adaa https://github.com/galaxyproject/galaxy/commit/0c91f65a99c43608faaa9f7b5046… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Change channel order in documentation Commit: 8a80b2dc712bd16465197799a4ef3cc8dab01bc9 https://github.com/galaxyproject/galaxy/commit/8a80b2dc712bd16465197799a4ef… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- change order in galaxy.ini Commit: 3d492657028b3a29c9e3707cb609db87f4a783f6 https://github.com/galaxyproject/galaxy/commit/3d492657028b3a29c9e3707cb609… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- change oder in docs Commit: f693643ea87dc807277cb6c2e8c3a2f9946fe5d4 https://github.com/galaxyproject/galaxy/commit/f693643ea87dc807277cb6c2e8c3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- change channel order in conda.py Commit: ad8d48c0a39de2afb360f58aee40f60f10dd25da https://github.com/galaxyproject/galaxy/commit/ad8d48c0a39de2afb360f58aee40… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3237 from galaxyproject/conda_channel change conda channel order Compare: https://github.com/galaxyproject/galaxy/compare/584114a46980...ad8d48c0a39d

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[galaxyproject/galaxy] f69364: change channel order in conda.py
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/conda_channel Home: https://github.com/galaxyproject/galaxy Commit: f693643ea87dc807277cb6c2e8c3a2f9946fe5d4 https://github.com/galaxyproject/galaxy/commit/f693643ea87dc807277cb6c2e8c3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- change channel order in conda.py

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[galaxyproject/galaxy] 3d4926: change oder in docs
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/conda_channel Home: https://github.com/galaxyproject/galaxy Commit: 3d492657028b3a29c9e3707cb609db87f4a783f6 https://github.com/galaxyproject/galaxy/commit/3d492657028b3a29c9e3707cb609… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- change oder in docs

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[galaxyproject/galaxy] 8a80b2: change order in galaxy.ini
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/conda_channel Home: https://github.com/galaxyproject/galaxy Commit: 8a80b2dc712bd16465197799a4ef3cc8dab01bc9 https://github.com/galaxyproject/galaxy/commit/8a80b2dc712bd16465197799a4ef… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- change order in galaxy.ini

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[galaxyproject/infrastructure-playbook] 36125a: Copies are bad
by GitHub 12 Dec '16

12 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 36125a0c0bd5de7dccebeb7ae1081e728bce5eba https://github.com/galaxyproject/infrastructure-playbook/commit/36125a0c0bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: A common_env/files/ssl/wildcard_cert.pem M galaxyenv/files/ssl/wildcard_cert.pem M taccenv/files/ssl/wildcard_cert.pem Log Message: ----------- Copies are bad

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