June 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 5b00fa: Fixes for Data Managers, plus allocate 128GB of me...
by GitHub 16 Jun '17

16 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5b00fa5d5c55915aaac7f440b1f074216be6a148 https://github.com/galaxyproject/usegalaxy-playbook/commit/5b00fa5d5c55915a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M env/common/templates/supervisor/galaxy_datamanager.j2 M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fixes for Data Managers, plus allocate 128GB of memory for the RNA STAR DM

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[galaxyproject/galaxy] 3384e1: correction of a typo leading to incomplete format ...
by GitHub 16 Jun '17

16 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3384e13744981a25f34433e80b3093cf3b495018 https://github.com/galaxyproject/galaxy/commit/3384e13744981a25f34433e80b30… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- correction of a typo leading to incomplete format string Commit: 2a5dc90003c6c787e2008140fa6b92cab387362c https://github.com/galaxyproject/galaxy/commit/2a5dc90003c6c787e2008140fa6b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M scripts/api/library_upload_dir.py Log Message: ----------- Merge pull request #4199 from FredericBGA/library_upload_dir Debug of script library_upload_dir.py Compare: https://github.com/galaxyproject/galaxy/compare/95a879c5e782...2a5dc90003c6

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[galaxyproject/usegalaxy-playbook] 1a3bfc: I forget why these variable names have changed but...
by GitHub 15 Jun '17

15 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1a3bfcec003a4827b75c28cc02a233fe65d952a1 https://github.com/galaxyproject/usegalaxy-playbook/commit/1a3bfcec003a4827… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- I forget why these variable names have changed but apparently I didn't finish changing them

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[galaxyproject/usegalaxy-playbook] 8f9080: Disable conda copying for per-job envs since all e...
by GitHub 15 Jun '17

15 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8f9080fbb5039af509b30a28a13c9af42f9054e8 https://github.com/galaxyproject/usegalaxy-playbook/commit/8f9080fbb5039af5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Disable conda copying for per-job envs since all envs are now mulled. always_symlink has also been enabled in _condarc

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[galaxyproject/galaxy] ebfdb5: Lint updateucsc.sh.sample
by GitHub 14 Jun '17

14 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebfdb598f63bd06925670e7c1764e1d1da740d05 https://github.com/galaxyproject/galaxy/commit/ebfdb598f63bd06925670e7c1764… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M cron/updateucsc.sh.sample Log Message: ----------- Lint updateucsc.sh.sample Commit: 404b855dd278760c625a6515279da6908ab9f9c6 https://github.com/galaxyproject/galaxy/commit/404b855dd278760c625a6515279d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M cron/updateucsc.sh.sample Log Message: ----------- Make updateucsc.sh.sample usable without any change Commit: 95a879c5e78283228c335e7c6d6e8e97916f1db1 https://github.com/galaxyproject/galaxy/commit/95a879c5e78283228c335e7c6d6e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M cron/updateucsc.sh.sample Log Message: ----------- Merge pull request #4192 from nsoranzo/updateucsc.sh Make updateucsc.sh.sample usable without any change Compare: https://github.com/galaxyproject/galaxy/compare/579b8b025cc5...95a879c5e782

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[galaxyproject/galaxy] 5a83e5: upload tool's test data into the History panel
by GitHub 14 Jun '17

14 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a83e56168369a3fccde6aae34015ffc21721188 https://github.com/galaxyproject/galaxy/commit/5a83e56168369a3fccde6aae3401… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-03-05 (Sun, 05 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M config/plugins/visualizations/charts/static/repository/utilities/jobs.js M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/tour_generator/config/tour_generator.yml A config/plugins/webhooks/tour_generator/helper/__init__.py A config/plugins/webhooks/tour_generator/static/script.js A config/plugins/webhooks/tour_generator/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js Log Message: ----------- upload tool's test data into the History panel Commit: 4fdb554629e10e4fd20a99806c9b2e8e883cb844 https://github.com/galaxyproject/galaxy/commit/4fdb554629e10e4fd20a99806c9b… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M .gitignore M config/galaxy.ini.sample A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css R config/plugins/webhooks/tour_generator/config/tour_generator.yml R config/plugins/webhooks/tour_generator/helper/__init__.py R config/plugins/webhooks/tour_generator/static/script.js R config/plugins/webhooks/tour_generator/static/styles.css Log Message: ----------- generate tool tours Commit: bef2e2fc00030dbcdf32acc3dcfe30175db80506 https://github.com/galaxyproject/galaxy/commit/bef2e2fc00030dbcdf32acc3dcfe… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- deal with different input types + bugfixes Commit: c7f3de9713c07ba51f61f7a2761e1a685b68d4eb https://github.com/galaxyproject/galaxy/commit/c7f3de9713c07ba51f61f7a2761e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve frontend script + bugfixes Commit: 73e90fc7f53fff6c9fdf901b9b06a66a801f0c6c https://github.com/galaxyproject/galaxy/commit/73e90fc7f53fff6c9fdf901b9b06… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js A client/galaxy/scripts/mvc/collection/base-creator.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/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js A client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/paired-collection-creator.less M client/galaxy/style/less/upload.less M client/package.json M client/webpack.config.js A config/build_sites.yml.sample M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map A 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tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/upload.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py R tools/filters/gff/sort_gtf.py M tools/filters/pasteWrapper.xml M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge branch 'dev' into auto_tour_generation # Conflicts: # static/maps/mvc/tool/tool-form-base.js.map # static/maps/mvc/tool/tool-form.js.map # static/scripts/bundled/analysis.bundled.js # static/scripts/bundled/analysis.bundled.js.map # static/scripts/bundled/libs.bundled.js # static/scripts/bundled/libs.bundled.js.map # static/scripts/bundled/login.bundled.js # static/scripts/bundled/login.bundled.js.map # static/scripts/mvc/tool/tool-form-base.js # static/scripts/mvc/tool/tool-form.js Commit: a3037742cf0a6521651dad63b5c9c466d0031da4 https://github.com/galaxyproject/galaxy/commit/a3037742cf0a6521651dad63b5c9… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- bugfixes after the previous merge Commit: ebcb2627dfa920d0b491191a961374fb3d091248 https://github.com/galaxyproject/galaxy/commit/ebcb2627dfa920d0b491191a9613… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/webhooks.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/webhooks.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 static/scripts/mvc/webhooks.js Log Message: ----------- tiny changes Commit: ebf1f3903caeeae7e712666228c34958cbfc4094 https://github.com/galaxyproject/galaxy/commit/ebf1f3903caeeae7e712666228c3… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- bugfixes and small improvements Commit: 934a26c195a983f64889bac6e25498ec16328e53 https://github.com/galaxyproject/galaxy/commit/934a26c195a983f64889bac6e254… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.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/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve the generator + bugfixes Commit: dc29a1a637c0274bceeb817ab64638a17464db6b https://github.com/galaxyproject/galaxy/commit/dc29a1a637c0274bceeb817ab646… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- add support for the 'conditional' input type Commit: 68ab3cfcac72cb759fc7941624d5a8e6a9ddb23e https://github.com/galaxyproject/galaxy/commit/68ab3cfcac72cb759fc7941624d5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M config/plugins/visualizations/charts/static/repository/utilities/jobs.js A config/plugins/webhooks/tour_generator/config/tour_generator.yml A config/plugins/webhooks/tour_generator/helper/__init__.py A config/plugins/webhooks/tour_generator/static/script.js A config/plugins/webhooks/tour_generator/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/webhooks.js.map M static/maps/onload.js.map M static/scripts/mvc/webhooks.js M static/scripts/onload.js M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- upload tool's test data into the History panel Commit: bb2c467c379a2780578e44551d9a447259256437 https://github.com/galaxyproject/galaxy/commit/bb2c467c379a2780578e44551d9a… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M .gitignore A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css R config/plugins/webhooks/tour_generator/config/tour_generator.yml R config/plugins/webhooks/tour_generator/helper/__init__.py R config/plugins/webhooks/tour_generator/static/script.js R config/plugins/webhooks/tour_generator/static/styles.css Log Message: ----------- generate tool tours Commit: e9accf5459d0a311cec590dcdeb4f07533d3a9aa https://github.com/galaxyproject/galaxy/commit/e9accf5459d0a311cec590dcdeb4… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- deal with different input types + bugfixes Commit: 5227e7b632ef3add1f8f0289c4caf6e926e53de6 https://github.com/galaxyproject/galaxy/commit/5227e7b632ef3add1f8f0289c4ca… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/onload.js Log Message: ----------- improve frontend script + bugfixes Commit: 31277edc6109aa97ab34ce6d851ade314b340dfa https://github.com/galaxyproject/galaxy/commit/31277edc6109aa97ab34ce6d851a… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- bugfixes after the previous merge Commit: e1f7875351c826bf503d00d6a43f3c415c601858 https://github.com/galaxyproject/galaxy/commit/e1f7875351c826bf503d00d6a43f… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/webhooks.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/webhooks.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/webhooks.js Log Message: ----------- tiny changes Commit: d6109ee1e81cb7b744309fca7cb7c0ef57ba6eb2 https://github.com/galaxyproject/galaxy/commit/d6109ee1e81cb7b744309fca7cb7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- bugfixes and small improvements Commit: e64cff4647ec2806b9b548274c363b7d022b6730 https://github.com/galaxyproject/galaxy/commit/e64cff4647ec2806b9b548274c36… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve the generator + bugfixes Commit: d253d7aa468bc9fe5d48ecea3be74059b9252300 https://github.com/galaxyproject/galaxy/commit/d253d7aa468bc9fe5d48ecea3be7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- add support for the 'conditional' input type Commit: 65a31e0e5dd7efd7c69a434100ff7d93eabee91c https://github.com/galaxyproject/galaxy/commit/65a31e0e5dd7efd7c69a434100ff… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- improve conditional input type message Commit: 17bb071721b83d63b3edf49ab1c509e4efb781ff https://github.com/galaxyproject/galaxy/commit/17bb071721b83d63b3edf49ab1c5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/onload.js Log Message: ----------- improve and simplify the main script Commit: 19567f48b846219a48eceb8d1a58cd29a659d5ba https://github.com/galaxyproject/galaxy/commit/19567f48b846219a48eceb8d1a58… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/webhooks.py M static/scripts/bundled/login.bundled.js Log Message: ----------- make client Commit: 64e91ddb8f0baf7a63c015bb7438fe19bd40bc7d https://github.com/galaxyproject/galaxy/commit/64e91ddb8f0baf7a63c015bb7438… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: 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/bundled/login.bundled.js Log Message: ----------- make client Commit: ed4fa0425efc9b719e923f6d0959e8098fd9b8e7 https://github.com/galaxyproject/galaxy/commit/ed4fa0425efc9b719e923f6d0959… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- fix a bug when a tour coudn't be ended after executing a tool Commit: 47a5f17089b696208cb5f432ade866c1d953601d https://github.com/galaxyproject/galaxy/commit/47a5f17089b696208cb5f432ade8… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- many improvements - show warning messages (not errors) - upload test datasets with a correct type according to the tool's .xml file (no 'auto' detection) - add more checks to improve the overall stability - fix tour messages - other bugfixes Commit: 542e396ddf48a8d9159ee0aa1e5137f307a6b8f4 https://github.com/galaxyproject/galaxy/commit/542e396ddf48a8d9159ee0aa1e51… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/onload.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/layout/menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/onload.js Log Message: ----------- introduce two new entry points: onload and tool-menu Commit: ce017c3fec9f1edd0d7858f408302b6962073657 https://github.com/galaxyproject/galaxy/commit/ce017c3fec9f1edd0d7858f40830… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- upload conditional test datasets Commit: c42941da04c94acec13598c8d6f8425c938ad548 https://github.com/galaxyproject/galaxy/commit/c42941da04c94acec13598c8d6f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.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/bundled/login.bundled.js.map M static/scripts/onload.js M templates/js-app.mako Log Message: ----------- Remove global Toastr addition, allow external requires through standard js-app entrypoint. Commit: d90a30f5eaf57eb0e3a1ba370406f393a066f96d https://github.com/galaxyproject/galaxy/commit/d90a30f5eaf57eb0e3a1ba370406… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/onload.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/bundled/login.bundled.js.map M static/scripts/onload.js M templates/js-app.mako Log Message: ----------- Merge pull request #4 from dannon/auto_tour_generation Toastr Loading fixes. Commit: ef0809c2eb95fb9bd740718a287d6548ceea0f3a https://github.com/galaxyproject/galaxy/commit/ef0809c2eb95fb9bd740718a287d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M config/plugins/visualizations/charts/static/repository/utilities/jobs.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/bundled/login.bundled.js.map Log Message: ----------- remove unnecessary whitespace fixes from otherwise untouched files Commit: 96d03c7c35eacb1d0e4bbf8675c51b3b429e53a1 https://github.com/galaxyproject/galaxy/commit/96d03c7c35eacb1d0e4bbf8675c5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-05-18 (Thu, 18 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/webhooks.js M 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Commit: 26f214257337c4546b9783bda8df9ac7e15b4444 https://github.com/galaxyproject/galaxy/commit/26f214257337c4546b9783bda8df… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CITATION M CONTRIBUTORS.md M Makefile M README.rst 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/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/citation/citation-view.js M 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static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-terminals.js A static/scripts/mvc/workflow/workflow.js A static/scripts/nls/de/locale.js A static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js M static/scripts/viz/phyloviz.js M static/style/blue/base.css M static/welcome.html.sample R templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/grid_base.mako M templates/sharing_base.mako M templates/show_params.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako R templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/data_manager/index.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/workflow/configure_menu.mako R templates/webapps/galaxy/workflow/list.mako R templates/webapps/galaxy/workflow/list_for_run.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py A test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/collection_creates_list_fail.xml A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml M test/galaxy_selenium/navigates_galaxy.py M test/qunit/test-data/bootstrapped.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge pull request #5 from dannon/auto_tour_generation Fixes .gitignore, merges dev. Commit: 579b8b025cc5242f1e32563cfb78ac3c354703d6 https://github.com/galaxyproject/galaxy/commit/579b8b025cc5242f1e32563cfb78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js 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.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/menu.js.map 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.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.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/layout/menu.js 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.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merge pull request #4019 from anatskiy/auto_tour_generation Tool-Describing-Tours Compare: https://github.com/galaxyproject/galaxy/compare/f58f372a26c4...579b8b025cc5

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[galaxyproject/galaxy] f7f28d: Build mulled images for Singularity on demand...
by GitHub 14 Jun '17

14 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7f28d606a17bc4020678d498895b3acdb955a9b https://github.com/galaxyproject/galaxy/commit/f7f28d606a17bc4020678d498895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py Log Message: ----------- Build mulled images for Singularity on demand... ... if a cached container for the tool in question cannot be found. This mirrors behavior for Docker and can be disabled by setting up a custom containers resolution file. This should also enable easy testing of tools with Planemo using Singularity. Commit: f58f372a26c43f1ef55e8193a324769285ba728a https://github.com/galaxyproject/galaxy/commit/f58f372a26c43f1ef55e8193a324… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py Log Message: ----------- Merge pull request #4185 from jmchilton/singularity_mulled_build Build mulled images for Singularity on demand... Compare: https://github.com/galaxyproject/galaxy/compare/3e36af050ff1...f58f372a26c4

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[galaxyproject/infrastructure-playbook] a78bc2: Ensure server options are applied to stratum 1s
by GitHub 13 Jun '17

13 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a78bc20a9bcb312f5d45eb5570f7966409d86e56 https://github.com/galaxyproject/infrastructure-playbook/commit/a78bc20a9bc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M roles/cvmfs/tasks/stratum1.yml Log Message: ----------- Ensure server options are applied to stratum 1s

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[galaxyproject/galaxy] 8d224e: Allow Galaxy to use cached mulled containers for S...
by GitHub 12 Jun '17

12 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d224edb5729114dd100fe730619d666df7e84dc https://github.com/galaxyproject/galaxy/commit/8d224edb5729114dd100fe730619… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Allow Galaxy to use cached mulled containers for Singularity. - Change undocumented (and probably unused) config option container_image_cache_path default to "database/contianer_cache". - Update container resolver framework to let plugins assert they only produce containers of a single type. - Update mulled container resolvers to indicate they produce Docker containers only - update names also. - Refactor mulled caching stuff to allow reuse with Singularity (where the names come from is different - but a lot of the logic is the same). - Add a cached singularity container resolver - that searches "config.container_image_cache_path/singularity/mulled" for an image with the correct name. Next up - similarly refactor the BuildMulledDockerContainerResolver to allow reuse and implement the BuildMulledSingularityContainerResolver. Commit: 49046336dce63c721077c779f832bf43fa020461 https://github.com/galaxyproject/galaxy/commit/49046336dce63c721077c779f832… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- fix CachedMulledSingularityContainerResolver Commit: d8c6838f21817690ed4a06b26cd64d7c39a990a3 https://github.com/galaxyproject/galaxy/commit/d8c6838f21817690ed4a06b26cd6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- pep8 fixes Commit: 3e36af050ff1b1e94dbae4a46607038bb16fd553 https://github.com/galaxyproject/galaxy/commit/3e36af050ff1b1e94dbae4a46607… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #4179 from jmchilton/singularity_mulled_cached Allow Galaxy to use cached mulled containers for Singularity. Compare: https://github.com/galaxyproject/galaxy/compare/f81c5bb1d957...3e36af050ff1

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[galaxyproject/galaxy] 55681f: Improve default handling of Singularity volumes.
by GitHub 12 Jun '17

12 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55681f6e2a4f8f5772a3979961d94344d7a45e2e https://github.com/galaxyproject/galaxy/commit/55681f6e2a4f8f5772a3979961d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-11 (Sun, 11 Jun 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Improve default handling of Singularity volumes. My understanding is that unlike Docker, Singularity doesn't allow a subdirectory to be mounted rw and its parent to be mounted ro - it will just be ro. This PR adjusts the default volume handling for Singularity to intelligently fallback to mounting parent directories as rw if their child directories are listed as being mounted rw. Ping @bgruening - is the above a description correct and does this approach work for you? Commit: 74333164dbc304d69434495516db6af958780a93 https://github.com/galaxyproject/galaxy/commit/74333164dbc304d69434495516db… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- pep fixes Commit: f81c5bb1d957b37ebe8d80cbef49d4a8a1284b7f https://github.com/galaxyproject/galaxy/commit/f81c5bb1d957b37ebe8d80cbef49… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #4180 from jmchilton/singularity_volumes Improve default handling of Singularity volumes. Compare: https://github.com/galaxyproject/galaxy/compare/d36c4053cd16...f81c5bb1d957

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