Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84c92590635358a0c0798dfc8aa8ae6d2b37660e https://github.com/galaxyproject/galaxy/commit/84c92590635358a0c0798dfc8aa8a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Bumping pysam to 0.12 *core*, without customization Commit: dadb3680f59e4646a53589d572d25df06d3850ed https://github.com/galaxyproject/galaxy/commit/dadb3680f59e4646a53589d572d25... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py Log Message: ----------- Separate non-stdlib pysam from other imports. Commit: ee120745afa1e30a58287591fa9fe5776c83abfa https://github.com/galaxyproject/galaxy/commit/ee120745afa1e30a58287591fa9fe... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Explicitly pin pysam to 0.12.0.1 Commit: c04cf6b228ec44ae1ec97820947954551cc1a33a https://github.com/galaxyproject/galaxy/commit/c04cf6b228ec44ae1ec9782094795... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Explicitly include PyPI as an --extra-index-url to pip so we can install from PyPI even when a package exists (but the correct version or architecture does not exist) on wheels.galaxyproject.org. Previously, PyPI was only checked after wheels.galaxyproject.org because pypiserver performs an automatic redirect to PyPI for any packages that do not exist in its index. Commit: 74665db45d10508030db8457529af4830a51caff https://github.com/galaxyproject/galaxy/commit/74665db45d10508030db8457529af... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M Makefile A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M 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test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/workflow_support.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.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_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joiner.xml M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.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_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.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/plotting/bar_chart.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/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into pysam012 Commit: 5581d270e7b921419f89d70ccda5c9d3eabe417b https://github.com/galaxyproject/galaxy/commit/5581d270e7b921419f89d70ccda5c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- All the way to 0.13 for pysam. Commit: a2c164a53ad99a0815cd3dbcc0b0b44605d4cfc2 https://github.com/galaxyproject/galaxy/commit/a2c164a53ad99a0815cd3dbcc0b0b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #4497 from dannon/pysam012 Bumping pysam to 0.13 *core*, without customization Compare: https://github.com/galaxyproject/galaxy/compare/7722fbaaad29...a2c164a53ad9