[galaxy-commits] [galaxyproject/galaxy] 87b798: FAST5 archive support

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87b798d40a5acb78ddf428d82639f2d5a7f40098 https://github.com/galaxyproject/galaxy/commit/87b798d40a5acb78ddf428d82639f... Author: jvolkening <jdv@base2bio.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- FAST5 archive support Commit: 9e6cb13e314d451cba7e0eaf841f05410ac19750 https://github.com/galaxyproject/galaxy/commit/9e6cb13e314d451cba7e0eaf841f0... Author: jvolkening <jdv@base2bio.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: A .ci/autopep8.sh M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A SECURITY_POLICY.md M client/bower.json A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M 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test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.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/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.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/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml 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/joinWrapper.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/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/trimmer.xml 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/wc_gnu.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml 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/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.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/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.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/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.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_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 tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fast5 Commit: 2fc60430a187cc4a95e2d935b89b65f52acd86b8 https://github.com/galaxyproject/galaxy/commit/2fc60430a187cc4a95e2d935b89b6... Author: jvolkening <jdv@base2bio.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix formatting to make tox happy Commit: f07c6a98431f1a4c2a2d81f99d3b54a23f0a901e https://github.com/galaxyproject/galaxy/commit/f07c6a98431f1a4c2a2d81f99d3b5... Author: jvolkening <jdv@base2bio.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- optimized sniffing, subclassed different tarball types Commit: 297d2353ce594b3325d029fb72c3ffd825c07f57 https://github.com/galaxyproject/galaxy/commit/297d2353ce594b3325d029fb72c3f... Author: jvolkening <jdv@base2bio.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz Log Message: ----------- add datatype tests Commit: 49258a7df8bb0f8c489c06dc2a77c27b2244b5f9 https://github.com/galaxyproject/galaxy/commit/49258a7df8bb0f8c489c06dc2a77c... Author: jvolkening <jdv@base2bio.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fixed sniff order and misc linting errors Commit: 08b5a47c396d38d288d54806edb87e9e717b799d https://github.com/galaxyproject/galaxy/commit/08b5a47c396d38d288d54806edb87... Author: jvolkening <jdv@base2bio.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/utils/uploadbox.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/utils/uploadbox.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/history/options-menu.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/utils/uploadbox.js A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_published_histories_grid.py M tools/data_source/upload.py M tools/filters/join.py M tools/filters/joiner.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fast5 Commit: 36a3a6b3d9c0b00c26ae861649983a441f725ae8 https://github.com/galaxyproject/galaxy/commit/36a3a6b3d9c0b00c26ae861649983... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz Log Message: ----------- Merge pull request #4569 from jvolkening/fast5 fast5_archive datatype Compare: https://github.com/galaxyproject/galaxy/compare/c0e2db2d98ea...36a3a6b3d9c0