galaxy-commits September 2016

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[galaxyproject/galaxy] 2eadec: Add flake8 pinning to Branch procedures
by GitHub 01 Oct '16

01 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2eadece71e8ff8cff76ed58d56cb5eba7ac99c87 https://github.com/galaxyproject/galaxy/commit/2eadece71e8ff8cff76ed58d56cb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Add flake8 pinning to Branch procedures Commit: 66a5bd45bd3c72e497b2098337de652b2c5d5f51 https://github.com/galaxyproject/galaxy/commit/66a5bd45bd3c72e497b2098337de… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2991 from nsoranzo/fix_for_2665 Add flake8 pinning to Branch procedures Compare: https://github.com/galaxyproject/galaxy/compare/c71c1300a2f2...66a5bd45bd3c

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[galaxyproject/galaxy] 1a91c6: Fix startswith method spelling
by GitHub 01 Oct '16

01 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a91c603892f7ea574197de67f738df6b7008dd8 https://github.com/galaxyproject/galaxy/commit/1a91c603892f7ea574197de67f73… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix startswith method spelling Introduced in commit 4b2e0c84e19001c8071b374a8e7daf609bb3aa88 Commit: c71c1300a2f2797a1009c1c86c9c9449b42e05d5 https://github.com/galaxyproject/galaxy/commit/c71c1300a2f2797a1009c1c86c9c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #2990 from nsoranzo/fix_for_2761 Fix startswith method spelling Compare: https://github.com/galaxyproject/galaxy/compare/a1158a79059a...c71c1300a2f2

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[galaxyproject/galaxy] 11b4f3: Fix import order and Python3 compatibility for too...
by GitHub 01 Oct '16

01 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 11b4f3a60c3f24ddbfdf1421391c9b443060a3cf https://github.com/galaxyproject/galaxy/commit/11b4f3a60c3f24ddbfdf1421391c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py Log Message: ----------- Fix import order and Python3 compatibility for tools/ xref #1715 Commit: a1158a79059a47cd928eee2acdbb81df9fbdabcb https://github.com/galaxyproject/galaxy/commit/a1158a79059a47cd928eee2acdbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge pull request #2983 from nsoranzo/python3 Fix import order and Python3 compatibility for tools/ Compare: https://github.com/galaxyproject/galaxy/compare/7dadb932d827...a1158a79059a

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[galaxyproject/usegalaxy-playbook] 994616: Convert Main Jetstream Pulsar from REST to MQ
by GitHub 30 Sep '16

30 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9946169077843dfbc2a0b6fa1522798855da64f7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9946169077843dfb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/host_vars/jetstream-iu0.galaxyproject.org.yml M production/host_vars/jetstream-tacc0.galaxyproject.org.yml R production/secret_host_vars/br005.bridges.psc.edu.yml R production/secret_host_vars/default.yml R production/secret_host_vars/login5.stampede.tacc.utexas.edu.yml A production/secret_vars/pulsarservers.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Convert Main Jetstream Pulsar from REST to MQ

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[galaxyproject/usegalaxy-playbook] 6510f5: Enable iobio on Main
by GitHub 30 Sep '16

30 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6510f50e8ec7b3991522261b42f832d80d525132 https://github.com/galaxyproject/usegalaxy-playbook/commit/6510f50e8ec7b399… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M files/galaxy/usegalaxy.org/config/tool_data_table_conf.xml M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Enable iobio on Main Commit: ffdd0f9e8a469969beb2c1527a63eddb9221c3c3 https://github.com/galaxyproject/usegalaxy-playbook/commit/ffdd0f9e8a469969… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M pulsar.yml M stage/host_vars/jetstream-iu0.galaxyproject.org.yml M stage/host_vars/jetstream-tacc0.galaxyproject.org.yml R stage/secret_host_vars/br005.bridges.psc.edu.yml R stage/secret_host_vars/default.yml R stage/secret_host_vars/login5.stampede.tacc.utexas.edu.yml A stage/secret_vars/pulsarservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Convert Test Jetstream Pulsar from REST to MQ Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1de0da3101cb...…

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[galaxyproject/galaxy] 9eba27: Optimized workflow invocation step update.
by GitHub 30 Sep '16

30 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9eba273202873abab5b9f302a9c2ae1cf21c7431 https://github.com/galaxyproject/galaxy/commit/9eba273202873abab5b9f302a9c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/model/mapping.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Optimized workflow invocation step update. Commit: 7dadb932d827ee168acefacbf041dad671d36c7f https://github.com/galaxyproject/galaxy/commit/7dadb932d827ee168acefacbf041… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M lib/galaxy/model/mapping.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #2973 from jmchilton/optimize_invocation_update Optimized workflow invocation step update. Compare: https://github.com/galaxyproject/galaxy/compare/1fee06e4e360...7dadb932d827

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[galaxyproject/galaxy] 7d2e3b: Update sqlalchemy to 1.0.15 (from 1.0.8). This is...
by GitHub 29 Sep '16

29 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d2e3be0b0e989a0ffe72bd8e974998a30353357 https://github.com/galaxyproject/galaxy/commit/7d2e3be0b0e989a0ffe72bd8e974… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Update sqlalchemy to 1.0.15 (from 1.0.8). This is likely the last 1.0 series release before we'll be able to upgrade to a live 1.1. Commit: 1fee06e4e360f442e2e621e084ca3b313b07138a https://github.com/galaxyproject/galaxy/commit/1fee06e4e360f442e2e621e084ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2979 from dannon/sqlalchemy_1.0.15 Update sqlalchemy to 1.0.15 (from 1.0.8). This is likely the last 1.… Compare: https://github.com/galaxyproject/galaxy/compare/fcd86c5e5862...1fee06e4e360

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[galaxyproject/galaxy] 0e3244: Bump pysam, remove 'already_compressed' usage due ...
by GitHub 29 Sep '16

29 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e324460165900cfba231bc729006f80f46b95e2 https://github.com/galaxyproject/galaxy/commit/0e324460165900cfba231bc72900… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Bump pysam, remove 'already_compressed' usage due to new wheel with autodetect Commit: 98ea43700dd635b6b0c7d6a274d5f3a22ba7829b https://github.com/galaxyproject/galaxy/commit/98ea43700dd635b6b0c7d6a274d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt Log Message: ----------- Update hashes for new pysam wheel. Commit: fcd86c5e586256438aa8b53035ecf2e1f1e98429 https://github.com/galaxyproject/galaxy/commit/fcd86c5e586256438aa8b53035ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #2953 from dannon/pysam_update_gx5 Bump pysam, remove 'already_compressed' usage due to new wheel with a… Compare: https://github.com/galaxyproject/galaxy/compare/860c2854b78a...fcd86c5e5862

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[galaxyproject/galaxy] 25ca45: Fuctional test case for testing column names as me...
by GitHub 29 Sep '16

29 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25ca456697f30671290859fbbcc14b126f2bbd51 https://github.com/galaxyproject/galaxy/commit/25ca456697f30671290859fbbcc1… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: A test/functional/tools/metadata_column_names.xml Log Message: ----------- Fuctional test case for testing column names as meta-data Commit: 8414e909a664855a82eda19b9a9fa26cf9178c3f https://github.com/galaxyproject/galaxy/commit/8414e909a664855a82eda19b9a9f… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Registration of metadata column name test into appropriate XML file - thanks to @nsoranzo Commit: ab68b951da7a766f06cc5fbbfaea34a2ea1b5dac https://github.com/galaxyproject/galaxy/commit/ab68b951da7a766f06cc5fbbfaea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M test/base/interactor.py M test/functional/tools/metadata_column_names.xml Log Message: ----------- Implement metadata testing for list metadata. Commit: 860c2854b78ac4c6aff2c8524a42225476f8b513 https://github.com/galaxyproject/galaxy/commit/860c2854b78ac4c6aff2c8524a42… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M test/base/interactor.py A test/functional/tools/metadata_column_names.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2970 from yhoogstrate/functional_test_metadata_columns Fuctional test case for testing column names as meta-data Compare: https://github.com/galaxyproject/galaxy/compare/695a759c9d83...860c2854b78a

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[galaxyproject/galaxy] 32064b: Lazy load workflow invocation steps
by GitHub 29 Sep '16

29 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 32064b338d619031112298dc489338cdbc67ec5b https://github.com/galaxyproject/galaxy/commit/32064b338d619031112298dc4893… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Lazy load workflow invocation steps Fix job handler going OOM when executing Job.set_final_state() for a step processing a 30K elements collection in parallel. Commit: 23fc1e5d577291a86ba9eed1e027ba7516bbfb9d https://github.com/galaxyproject/galaxy/commit/23fc1e5d577291a86ba9eed1e027… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/model/mapping.py Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/model/mapping.py Commit: 695a759c9d8301ef447cd30a2c2efd4ef958e79e https://github.com/galaxyproject/galaxy/commit/695a759c9d8301ef447cd30a2c2e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #2978 from nsoranzo/lazy_workflow_invocation Lazy load workflow invocation steps Compare: https://github.com/galaxyproject/galaxy/compare/10703fac3a00...695a759c9d83

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galaxy-commits September 2016