- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 11b4f3: Fix import order and Python3 compatibility for too...
by GitHub 30 Sep '16

30 Sep '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 29 Sep '16

29 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 29 Sep '16

29 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 29 Sep '16

29 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 28 Sep '16

28 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 28 Sep '16

28 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 28 Sep '16

28 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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[galaxyproject/galaxy] 8054da: Update issues.rst
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8054da9fb4d858b7ff9dd461f8baa923fea99425 https://github.com/galaxyproject/galaxy/commit/8054da9fb4d858b7ff9dd461f8ba… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Update issues.rst Commit: 10703fac3a00a854bb3d4d548ab1dd22485199c5 https://github.com/galaxyproject/galaxy/commit/10703fac3a00a854bb3d4d548ab1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Merge pull request #2976 from martenson/issues-on-par-with-reality bring issues.rst on par with reality Compare: https://github.com/galaxyproject/galaxy/compare/aa70a97e1e57...10703fac3a00

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[galaxyproject/galaxy] d2ac5a: adding admin feature to allow user to turn on or o...
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d2ac5a001c1f2d17034622c5ad9298899b370ed3 https://github.com/galaxyproject/galaxy/commit/d2ac5a001c1f2d17034622c5ad92… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py M templates/webapps/galaxy/library/common/common.mako M tools/data_source/upload.py Log Message: ----------- adding admin feature to allow user to turn on or off line ending conversion Commit: bede2907b99951163b8cee69f79405abf4e44e1a https://github.com/galaxyproject/galaxy/commit/bede2907b99951163b8cee69f794… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M templates/webapps/galaxy/library/common/common.mako M tools/data_source/upload.py Log Message: ----------- added some changes to fix Commit: 8d8ea2158b5a7ba763985f369719f18c7b4230cc https://github.com/galaxyproject/galaxy/commit/8d8ea2158b5a7ba763985f369719… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- remove cProfile import Commit: c53585e8b5227e9d9f3536fa1434ae74acc0ef68 https://github.com/galaxyproject/galaxy/commit/c53585e8b5227e9d9f3536fa1434… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- added cProfile Commit: 66e3f8540f4dff918a90c2d02eca4a3f46f7fbdd https://github.com/galaxyproject/galaxy/commit/66e3f8540f4dff918a90c2d02eca… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- removed traces of cProfile and use Commit: bc1be68bb6f0eef840465dd2b578136d0094ae20 https://github.com/galaxyproject/galaxy/commit/bc1be68bb6f0eef840465dd2b578… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- added the extra blank line Commit: e85cd284d099af16329d6592b46dc3d6ce37dba4 https://github.com/galaxyproject/galaxy/commit/e85cd284d099af16329d6592b46d… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- fixed the line tabs Commit: aa70a97e1e570507121320d9f2370265fd25fca8 https://github.com/galaxyproject/galaxy/commit/aa70a97e1e570507121320d9f237… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py M templates/webapps/galaxy/library/common/common.mako Log Message: ----------- Merge pull request #2819 from SANBI-SA/upload_admin_line_endings Functionality to allow admins to switch on/off the line endings conversion on import Compare: https://github.com/galaxyproject/galaxy/compare/8ff8af7b248b...aa70a97e1e57

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[galaxyproject/galaxy] 7ecf93: Fix import order in containers.py (broken in cad40...
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ecf9377bf3780faa2bb93594cf41435a15ff40a https://github.com/galaxyproject/galaxy/commit/7ecf9377bf3780faa2bb93594cf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix import order in containers.py (broken in cad4002efed5547ccc1f89a3a45d2d4b9b12f76d). Commit: 8ff8af7b248b79436113e03d3c01e2cc4cd2a88c https://github.com/galaxyproject/galaxy/commit/8ff8af7b248b79436113e03d3c01… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2975 from jmchilton/fix_import_order Fix import order in containers.py Compare: https://github.com/galaxyproject/galaxy/compare/002d974f8ada...8ff8af7b248b

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[galaxyproject/galaxy] cad400: Allow more rich container description in job_conf....
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cad4002efed5547ccc1f89a3a45d2d4b9b12f76d https://github.com/galaxyproject/galaxy/commit/cad4002efed5547ccc1f89a3a45d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Allow more rich container description in job_conf.xml. Commit: 6466ffe31e250575cc4ca278b0730ba7f1207e0d https://github.com/galaxyproject/galaxy/commit/6466ffe31e250575cc4ca278b073… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Allow more configurability in container descriptions. <container> descriptions (in job_conf.xml or in tool files) can now specify a few more options - including if Galaxy should perform tool dependency resolution (using the resolve_dependencies attribute - defaults to false) and job script shell (defaults to /bin/sh - but for containers with bash this should be overridden and set to /bin/bash). This should enable use cases such as that outlined in #2764. Commit: 002d974f8adae4cfc52c434c46c4966ac90918bd https://github.com/galaxyproject/galaxy/commit/002d974f8adae4cfc52c434c46c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Merge pull request #2790 from jmchilton/docker_container_xml More configurability for containerized jobs Compare: https://github.com/galaxyproject/galaxy/compare/0df6ff9f2d7d...002d974f8ada

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[galaxyproject/usegalaxy-playbook] bdc76b: Updated integrated tool panel for Trinity on Main
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bdc76b2c117d48fe0ce1af06c45c9ad738f3e220 https://github.com/galaxyproject/usegalaxy-playbook/commit/bdc76b2c117d48fe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- Updated integrated tool panel for Trinity on Main Commit: 1de0da3101cb79a84451e43a44d638bddd5c47df https://github.com/galaxyproject/usegalaxy-playbook/commit/1de0da3101cb79a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M production/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- Install dependency_resolvers_conf.xml on Bridges for Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/29f7ff12d0cb...…

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[galaxyproject/usegalaxy-playbook] 18340f: Update Main
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 18340f9502b4ce066d59de8cf388ecac1cf02a14 https://github.com/galaxyproject/usegalaxy-playbook/commit/18340f9502b4ce06… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main Commit: 29f7ff12d0cb80f1a117a428ef4e2efaa00e455a https://github.com/galaxyproject/usegalaxy-playbook/commit/29f7ff12d0cb80f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Cut 'n paste error from Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4a8302799db4...…

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[galaxyproject/usegalaxy-playbook] 4a8302: Apparently I never committed the galaxy_url change...
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4a8302799db46e7630c5ffdd4c8ce33c4503e47c https://github.com/galaxyproject/usegalaxy-playbook/commit/4a8302799db46e76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Apparently I never committed the galaxy_url changes? Also, change Bridges native spec for updated dynamic rule

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[galaxyproject/usegalaxy-playbook] 07e54c: Enable iobio on Test
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 07e54c5c412ef28cc589e18178854fa4bfc8e911 https://github.com/galaxyproject/usegalaxy-playbook/commit/07e54c5c412ef28c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M files/galaxy/test.galaxyproject.org/config/tool_data_table_conf.xml M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 Log Message: ----------- Enable iobio on Test

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[galaxyproject/galaxy] 8b452c: Remove invalid attribute metadata_name from param ...
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b452c9dc3dca9c4ba8804e0a3e6edd8d06946c0 https://github.com/galaxyproject/galaxy/commit/8b452c9dc3dca9c4ba8804e0a3e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Remove invalid attribute metadata_name from param examples in XSD docs. Pointed out by @peterjc in https://github.com/galaxyproject/tools-iuc/pull/964#issuecomment-249632638. Commit: 0df6ff9f2d7d841b322ee690a84ec8baa822b336 https://github.com/galaxyproject/galaxy/commit/0df6ff9f2d7d841b322ee690a84e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #2974 from jmchilton/schema_fix_0 Remove invalid attribute metadata_name from param examples in XSD docs. Compare: https://github.com/galaxyproject/galaxy/compare/051d2b285487...0df6ff9f2d7d

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[galaxyproject/galaxy] 750cb7: encourage bug reporting in tool schema
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 750cb7c5843fee4c82f7b028fa59d718a0629927 https://github.com/galaxyproject/galaxy/commit/750cb7c5843fee4c82f7b028fa59… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M doc/schema_template.md Log Message: ----------- encourage bug reporting in tool schema Commit: 051d2b285487fb99a065448b20f69f0d82d3a100 https://github.com/galaxyproject/galaxy/commit/051d2b285487fb99a065448b20f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M doc/schema_template.md Log Message: ----------- Merge pull request #2972 from martenson/tool-schema-report encourage bug reporting in tool schema document Compare: https://github.com/galaxyproject/galaxy/compare/780473a751ae...051d2b285487

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[galaxyproject/galaxy] 1d1620: Refactor recent toolbox changes for galaxy-lib.
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d16200759895b6ede6c38655d085fa7bb0a1e17 https://github.com/galaxyproject/galaxy/commit/1d16200759895b6ede6c38655d08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Refactor recent toolbox changes for galaxy-lib. The abstracttoolbox class is supposed to shield Galaxy from the internals of the toolbox organization and vice versa, so having a reload method that uses Galaxy-specific queueing stuff is less than ideal. The concrete toolbox class is where I have been putting such functionality. In addition to this being the abstract design I prefer, it is definitely needed for galaxy-lib which contains the abstracttoolbox but not the concrete toolbox or the queue worker functionality. xref #2840 Commit: 780473a751ae52868e29b4e34ba2b0894598dc7b https://github.com/galaxyproject/galaxy/commit/780473a751ae52868e29b4e34ba2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #2971 from jmchilton/galaxy-lib-import-fix Refactor recent toolbox changes for galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/7f19ba817c4d...780473a751ae

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[galaxyproject/galaxy] d7ab1c: UI, Modal: re-build dom on render
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: d7ab1c5cfbfcdff3ce3e201f6fb0684fdb914096 https://github.com/galaxyproject/galaxy/commit/d7ab1c5cfbfcdff3ce3e201f6fb0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- UI, Modal: re-build dom on render Moves templating to render (and updates dom node attributes after) to reset modal and prevent inline styling and other modifications to the singleton from persisting between calls to show. Commit: 04d62e242412d0eb6e739f3577256d99b1aaa5bf https://github.com/galaxyproject/galaxy/commit/04d62e242412d0eb6e739f357725… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge pull request #2955 from carlfeberhard/fix.modal-resetting [16.07] UI, Modal: re-build dom on render Compare: https://github.com/galaxyproject/galaxy/compare/e667f9f36038...04d62e242412

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[galaxyproject/galaxy] 9c4310: Remove html builders for tool parameters, strip ru...
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c43103630eb8bceb10021b282b8296218c04729 https://github.com/galaxyproject/galaxy/commit/9c43103630eb8bceb10021b282b8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove html builders for tool parameters, strip run workflow mako Commit: cd93da35c11f9374c5ffd03a44cbf33876dffb29 https://github.com/galaxyproject/galaxy/commit/cd93da35c11f9374c5ffd03a44cb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py R templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- Remove old run controller Commit: 289ac4845ad79cc7ee2079784d31182d3df23027 https://github.com/galaxyproject/galaxy/commit/289ac4845ad79cc7ee2079784d31… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unused checked list state for booleans Commit: 9f6a88a28f968a03301e8a516f10a5322bc77f4e https://github.com/galaxyproject/galaxy/commit/9f6a88a28f968a03301e8a516f10… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unused to_dict parameters Commit: cd91e3141c7d031b092091ce22345d87b8aa76d2 https://github.com/galaxyproject/galaxy/commit/cd91e3141c7d031b092091ce2234… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Rename regex parameter, fix spacing Commit: b38b9fe2e1663d724651a0c6e1aa78e87acaa43d https://github.com/galaxyproject/galaxy/commit/b38b9fe2e1663d724651a0c6e1aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove comment Commit: 13f498568c505b24f1b9753aaf158be324542219 https://github.com/galaxyproject/galaxy/commit/13f498568c505b24f1b9753aaf15… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove unused repeat handling Commit: d5ca00d6892874dc7da54be0a45da3cea4acb878 https://github.com/galaxyproject/galaxy/commit/d5ca00d6892874dc7da54be0a45d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Adjust first half of test cases in basic paramter handling Commit: 143a3ecffcc8da4469245b40336901f944b531e0 https://github.com/galaxyproject/galaxy/commit/143a3ecffcc8da4469245b403369… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix test cases Commit: adfaa948e9f65c07bf8cf8a67791bb3dd0e30bc6 https://github.com/galaxyproject/galaxy/commit/adfaa948e9f65c07bf8cf8a67791… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused imports Commit: c61933d1b1c0289735945bf97bf8b1f4bf5e5fc8 https://github.com/galaxyproject/galaxy/commit/c61933d1b1c0289735945bf97bf8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Fix dataset parameter tests Commit: 979bdd44c60d5aab27e472b19afa8dd704ee195a https://github.com/galaxyproject/galaxy/commit/979bdd44c60d5aab27e472b19afa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix drilldown tests Commit: 05923e210c41e0f3a6d14a3bd914356c042f4670 https://github.com/galaxyproject/galaxy/commit/05923e210c41e0f3a6d14a3bd914… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Undo name change for workflow regex Commit: 9863e35368066975fe049adee716c5cabad4c60f https://github.com/galaxyproject/galaxy/commit/9863e35368066975fe049adee716… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Attempt to remove value_mapper parsing Commit: 29cfd1635879987de9d1efc49d704894454a3ddf https://github.com/galaxyproject/galaxy/commit/29cfd1635879987de9d1efc49d70… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Fix test_parameter_parsing Commit: 474c9a26c495ddddeb6ba7c1966de6ae32cedea7 https://github.com/galaxyproject/galaxy/commit/474c9a26c495ddddeb6ba7c1966d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako M test/unit/tools/test_data_parameters.py Log Message: ----------- Fix toolshed tool form preview, import order Commit: 6b40607e7917b98c481c4e47ac31d31698ce2660 https://github.com/galaxyproject/galaxy/commit/6b40607e7917b98c481c4e47ac31… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove debug output Commit: 0ef6f7826c621235beef70e8e4c3352d2ab2e2b6 https://github.com/galaxyproject/galaxy/commit/0ef6f7826c621235beef70e8e4c3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Move controller build endpoint to api Commit: 057485b6f6a8c545478907d01bd6ceadfea0d1f6 https://github.com/galaxyproject/galaxy/commit/057485b6f6a8c545478907d01bd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Import exception, fix parameter names Commit: a537daa9ed24fe4a4fd7c9e7c54ba30f6de6e156 https://github.com/galaxyproject/galaxy/commit/a537daa9ed24fe4a4fd7c9e7c54b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Move run form model builder to workflow data manager Commit: b2014fe44ce7b5af42956cf74cd6e75c51a8df0f https://github.com/galaxyproject/galaxy/commit/b2014fe44ce7b5af42956cf74cd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Disable target history specification for run workflow form Commit: 2c79755ba2fb752418d7405efdfdcd46bf14d8a4 https://github.com/galaxyproject/galaxy/commit/2c79755ba2fb752418d7405efdfd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix stored/workflow handling Commit: 667d5e83cb6ccb7b46084b73101cb85cc81dd9fa https://github.com/galaxyproject/galaxy/commit/667d5e83cb6ccb7b46084b73101c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Fix value parsing Commit: 21b5246c913fbf5ae8361f359e17252718f1f87d https://github.com/galaxyproject/galaxy/commit/21b5246c913fbf5ae8361f359e17… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove unused data manager Commit: c5d00518fe409d4876c18ceaeeef2ad5b6829385 https://github.com/galaxyproject/galaxy/commit/c5d00518fe409d4876c18ceaeeef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix error messages Commit: 86719ce90e2cb8ee8439b2f4e8a947cc239e1957 https://github.com/galaxyproject/galaxy/commit/86719ce90e2cb8ee8439b2f4e8a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove redundant imports Commit: 675398c91263eaed37007b76e4856a6d81f888a3 https://github.com/galaxyproject/galaxy/commit/675398c91263eaed37007b76e485… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use message exception to parse errors Commit: a0da06d842a6488ee355c0cf37c06f7ffb8ee837 https://github.com/galaxyproject/galaxy/commit/a0da06d842a6488ee355c0cf37c0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Revise comment Commit: 05b1c988961e9e002e10d4e4cc21f49ff4ab958a https://github.com/galaxyproject/galaxy/commit/05b1c988961e9e002e10d4e4cc21… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Add basic step version changes notification Commit: 680e34c1adf87e3f6181bc2d6508f3f5ab84c903 https://github.com/galaxyproject/galaxy/commit/680e34c1adf87e3f6181bc2d6508… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix form preview height style Commit: 80b5e5da91cdf65b8f06e75a9a6b2c202b94d409 https://github.com/galaxyproject/galaxy/commit/80b5e5da91cdf65b8f06e75a9a6b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-portlet.js M static/style/blue/base.css Log Message: ----------- Remove unused portlet footer Commit: 1ab673a4ed5de36db49e24edae821d226040d183 https://github.com/galaxyproject/galaxy/commit/1ab673a4ed5de36db49e24edae82… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Fix padding distance Commit: 9dc412921e5b5446aa4493aca8c7c0105f7d0725 https://github.com/galaxyproject/galaxy/commit/9dc412921e5b5446aa4493aca8c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix bottom margin Commit: 7a736818a6c32615c396a2a18d9ebd884ddccebb https://github.com/galaxyproject/galaxy/commit/7a736818a6c32615c396a2a18d9e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M test/qunit/tests/form_tests.js Log Message: ----------- Avoid inheritance in tool-form view Avoid inheritance for workflow editor form Fix test cases Commit: 42ebe00c060d6fcbc69fd16973995c33aba48207 https://github.com/galaxyproject/galaxy/commit/42ebe00c060d6fcbc69fd1697399… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Add listener to properly clean up deferred form building processes Commit: 2cf7b8ee15856626bff5dfad735023a43ace978b https://github.com/galaxyproject/galaxy/commit/2cf7b8ee15856626bff5dfad7350… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/utils/utils.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/tool/tool-form-base.js M static/scripts/utils/utils.js Log Message: ----------- Fix status handling for ajax requests Commit: e3346e1d273b277445844e38e9e8d29873b4d619 https://github.com/galaxyproject/galaxy/commit/e3346e1d273b277445844e38e9e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M .gitignore M Makefile A doc/parse_gx_xsd.py A doc/schema_template.md M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M scripts/bootstrap_history.py M scripts/tool_shed/build_ts_whoosh_index.py M templates/webapps/galaxy/dataset/copy_view.mako M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'dev' into strip_run_form_mako Commit: 7f19ba817c4d8e7d82380bd6fe8d03a7247488f3 https://github.com/galaxyproject/galaxy/commit/7f19ba817c4d8e7d82380bd6fe8d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-25 (Sun, 25 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/utils/utils.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/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/qunit/tests/form_tests.js M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parameter_parsing.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #2935 from guerler/strip_run_form_mako Strip workflow run mako Compare: https://github.com/galaxyproject/galaxy/compare/cbb957028f0c...7f19ba817c4d

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[galaxyproject/galaxy] e18d4e: UI, datasets: fix optional column form values
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: e18d4ed33b8b453229f969f2d05c997b2fa7fe96 https://github.com/galaxyproject/galaxy/commit/e18d4ed33b8b453229f969f2d05c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- UI, datasets: fix optional column form values Updates metadata column checkbox flag from 'true' to '__NOTHING__' to reflect newer form_builder values. Fixes #2175 Commit: e667f9f360388839d723421b884836acb6974e6c https://github.com/galaxyproject/galaxy/commit/e667f9f360388839d723421b8848… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-25 (Sun, 25 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #2960 from carlfeberhard/fix.bed-columns [16.07] UI, datasets: fix optional column form values Compare: https://github.com/galaxyproject/galaxy/compare/26d381c9a5d7...e667f9f36038

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[galaxyproject/usegalaxy-playbook] e703f7: Bridges for Main
by GitHub 23 Sep '16

23 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e703f798aa6e2586d5b3481ef830f4b3d0cf6d83 https://github.com/galaxyproject/usegalaxy-playbook/commit/e703f798aa6e2586… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M files/galaxy/usegalaxy.org/config/job_resource_params_conf.xml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Bridges for Main

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[galaxyproject/galaxy] b83f0a: Fix whoosh indexing.
by GitHub 23 Sep '16

23 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b83f0a10247119ef18bf72688d4e0bb8cfee8e36 https://github.com/galaxyproject/galaxy/commit/b83f0a10247119ef18bf72688d4e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Fix whoosh indexing. Commit: 2c8a5d9d58c49c662aed4193f71caaf3fafe5651 https://github.com/galaxyproject/galaxy/commit/2c8a5d9d58c49c662aed4193f71c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Correct import order. Commit: 092a7307c21afa8d66129dca23567b49a540d66a https://github.com/galaxyproject/galaxy/commit/092a7307c21afa8d66129dca2356… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #2949 from davebx/backport_whoosh [16.07] Fix missing import in whoosh indexing script Commit: 7a604c67d95f51f0afdaa980d01ab4061b4631f0 https://github.com/galaxyproject/galaxy/commit/7a604c67d95f51f0afdaa980d01a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/317fb472c962...7a604c67d95f

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[galaxyproject/galaxy] b83f0a: Fix whoosh indexing.
by GitHub 23 Sep '16

23 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: b83f0a10247119ef18bf72688d4e0bb8cfee8e36 https://github.com/galaxyproject/galaxy/commit/b83f0a10247119ef18bf72688d4e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Fix whoosh indexing. Commit: 2c8a5d9d58c49c662aed4193f71caaf3fafe5651 https://github.com/galaxyproject/galaxy/commit/2c8a5d9d58c49c662aed4193f71c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Correct import order. Commit: 092a7307c21afa8d66129dca23567b49a540d66a https://github.com/galaxyproject/galaxy/commit/092a7307c21afa8d66129dca2356… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #2949 from davebx/backport_whoosh [16.07] Fix missing import in whoosh indexing script Compare: https://github.com/galaxyproject/galaxy/compare/3b3e2e3358aa...092a7307c21a

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