September 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6a266a: More tests for runtime workflow parameters.
by GitHub 07 Sep '18

07 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a266a19a947e853b37ce20eee9fc1f775b5f550 https://github.com/galaxyproject/galaxy/commit/6a266a19a947e853b37ce20eee9f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- More tests for runtime workflow parameters. Commit: 7806a84d1c22ba6f8b580fee78cb6bf594967936 https://github.com/galaxyproject/galaxy/commit/7806a84d1c22ba6f8b580fee78cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/base/workflow_fixtures.py M test/selenium_tests/test_workflow_run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Implement runtime parameters in nested workflows. Commit: fc75d4f9fbf8c6406d80873570392e925e40f56c https://github.com/galaxyproject/galaxy/commit/fc75d4f9fbf8c6406d8087357039… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M test/api/test_workflows.py M test/base/workflow_fixtures.py Log Message: ----------- Test case - verify step parameters replace after workflow invoke pauses. Commit: da18624067c819d4940658d9a5675c84977a2b3d https://github.com/galaxyproject/galaxy/commit/da18624067c819d4940658d9a567… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_workflow_run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #6664 from jmchilton/runtime_parameters Implement runtime parameters for subworkflows. Compare: https://github.com/galaxyproject/galaxy/compare/5c54793ddfbd...da18624067c8 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 03f124: Update Test
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 03f1247cf1dcf1bcf38608323d9aa7fed0206b86 https://github.com/galaxyproject/usegalaxy-playbook/commit/03f1247cf1dcf1bc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Conflicts: env/test/files/galaxy/galaxy_version.yml **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] a4495c: Update Test
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/swarmscale-2.0 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4495ccc4a809d6247edd1c4137b26d8d3f191a3 https://github.com/galaxyproject/usegalaxy-playbook/commit/a4495ccc4a809d62… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 81dc9b: Update Jetstream image
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 81dc9b98f0c5bf6ccb8521c6aa959d1c1124c917 https://github.com/galaxyproject/infrastructure-playbook/commit/81dc9b98f0c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M roles/slurmscale/files/group_vars/all/spawn.yml Log Message: ----------- Update Jetstream image **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 64652c: Drop wait from cached job tests
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64652c28cf7ea88195b1c9008c46137c3bb3644a https://github.com/galaxyproject/galaxy/commit/64652c28cf7ea88195b1c9008c46… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Drop wait from cached job tests Commit: 31d850b64484dd4f418a27c9313a954f89e37d7d https://github.com/galaxyproject/galaxy/commit/31d850b64484dd4f418a27c9313a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py Log Message: ----------- Make discovery of cachable jobs more robust We update the actually used version once the job inputs are ready. This allows finding jobs when a dataset is being new / being updated while the job is new. This is also more accurate since we record the dataset versino that is actually being used when the tool is being evaluated. This should allow chaching when simultaneously running workflows that share steps. Commit: a0982c1b900111d0b2a4add372f0caef0686a000 https://github.com/galaxyproject/galaxy/commit/a0982c1b900111d0b2a4add372f0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Only create HDA history if HDA columns have changed This creates fewer versions because we ignore relationship changes. Commit: 5c54793ddfbd86875322280ab74041152e6c8a40 https://github.com/galaxyproject/galaxy/commit/5c54793ddfbd86875322280ab740… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6669 from mvdbeek/fix_cache_tests Increase robustness and accuracy of job search / cache use Compare: https://github.com/galaxyproject/galaxy/compare/89405fae9435...5c54793ddfbd **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 432c0d: Install logflux for nginx rate limit logs
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/swarmscale-2.0 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 432c0d613aeac21334211f28a0ffc7c353231c1f https://github.com/galaxyproject/usegalaxy-playbook/commit/432c0d613aeac213… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M env/common/stack.yml A env/test/group_vars/logfluxservers.yml M env/test/inventory A roles/logflux/defaults/main.yml A roles/logflux/handlers/main.yml A roles/logflux/tasks/main.yml A roles/logflux/templates/logflux.service.j2 A roles/logflux/templates/rsyslog.conf.j2 Log Message: ----------- Install logflux for nginx rate limit logs **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9f14fc: Add Seurat datatype: rdata.seurat
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f14fcb1005452bae314eeebb324351a98510204 https://github.com/galaxyproject/galaxy/commit/9f14fcb1005452bae314eeebb324… Author: Maria Doyle <maria.doyle(a)petermac.org> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add Seurat datatype: rdata.seurat Commit: 89405fae9435bfc344f10c4155736d2810df84cd https://github.com/galaxyproject/galaxy/commit/89405fae9435bfc344f10c415573… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6648 from mblue9/add_seurat_datatype Add Seurat datatype: rdata.seurat Compare: https://github.com/galaxyproject/galaxy/compare/6787dbc9ee90...89405fae9435 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 51b4de: Allow running scripts/galaxy-main without Galaxy o...
by GitHub 06 Sep '18

06 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51b4def4ec005b136707bff38611ed09ba6db2ff https://github.com/galaxyproject/galaxy/commit/51b4def4ec005b136707bff38611… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M scripts/galaxy-main Log Message: ----------- Allow running scripts/galaxy-main without Galaxy on $PYTHONPATH Commit: 4ed9df9a947563a5fca4e07caad1b6a19cd6a845 https://github.com/galaxyproject/galaxy/commit/4ed9df9a947563a5fca4e07caad1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M scripts/galaxy-main Log Message: ----------- Set config builder attributes before they're referenced in app_kwds() Commit: 923ed2ed493a9575473b58da52d80de2d58ab41a https://github.com/galaxyproject/galaxy/commit/923ed2ed493a9575473b58da52d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M scripts/galaxy-main Log Message: ----------- Simplify importing from galaxy lib Commit: e14b871eb9ce577a8ee107728e4acb41028ddaa1 https://github.com/galaxyproject/galaxy/commit/e14b871eb9ce577a8ee107728e4a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Add test for scripts/galaxy-main Commit: 6787dbc9ee90662e2bf52b596d787ea0d66f88bd https://github.com/galaxyproject/galaxy/commit/6787dbc9ee90662e2bf52b596d78… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M scripts/galaxy-main M test/integration/test_scripts.py Log Message: ----------- Merge pull request #6642 from natefoo/galaxy-main-import Allow running scripts/galaxy-main without Galaxy on sys.path Compare: https://github.com/galaxyproject/galaxy/compare/7f1f8a7a4eda...6787dbc9ee90 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 8affe2: py3: fix secure_hash_message_digest.py
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8affe206df782658dbc388d5ffe1c5c1d6a136ef https://github.com/galaxyproject/galaxy/commit/8affe206df782658dbc388d5ffe1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/secure_hash_message_digest.py Log Message: ----------- py3: fix secure_hash_message_digest.py Commit: df5cab38ae35a38e1d7486d8c2fc0c8f452ed32e https://github.com/galaxyproject/galaxy/commit/df5cab38ae35a38e1d7486d8c2fc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/wc_gnu.xml Log Message: ----------- Fix wc_gnu test 1; list comprehensions are function objects on py3 and can't access outer local namespace Commit: 6352a0ef3ea5d80771276bcf4b928dda3acdbc08 https://github.com/galaxyproject/galaxy/commit/6352a0ef3ea5d80771276bcf4b92… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/util/ucsc.py Log Message: ----------- Fix wiggle2simple1 Commit: 36c74bbafa972f0e76ad8bf7befa23090eb8d92e https://github.com/galaxyproject/galaxy/commit/36c74bbafa972f0e76ad8bf7befa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- Fix maf_utilities comparison Commit: 6c7203b83d19d1f79bd6b1790ce24e9507931257 https://github.com/galaxyproject/galaxy/commit/6c7203b83d19d1f79bd6b1790ce2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/plotting/boxplot.xml Log Message: ----------- py3: Fix qual_stats_boxplot Commit: 6405aeb86c2240e010fadcd4e4758feccabba218 https://github.com/galaxyproject/galaxy/commit/6405aeb86c2240e010fadcd4e475… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Comment out tests with unavailable test data Commit: 8190c3fc4389299c8d9484bf3b3409b5cea51921 https://github.com/galaxyproject/galaxy/commit/8190c3fc4389299c8d9484bf3b34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/join.py Log Message: ----------- Fix the join1 tool Commit: 3fcf1e336dd2e32b0199388528078ce19ab7d98b https://github.com/galaxyproject/galaxy/commit/3fcf1e336dd2e32b019938852807… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/solid_tools/solid_qual_stats.py Log Message: ----------- Fix solid_qual_stats.py Commit: 2d732715ff50241fcddfab58795306a3880bd3c3 https://github.com/galaxyproject/galaxy/commit/2d732715ff50241fcddfab587953… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/grouping.py Log Message: ----------- Fix grouping tool Commit: 8889bd0a3d93266893a21dedefa9f93b8e51e8ef https://github.com/galaxyproject/galaxy/commit/8889bd0a3d93266893a21dedefa9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/senatag.py Log Message: ----------- Fix various things about the hgv_ldtools tool Unfortnately this doens't produce the test-data output on python 3 and so I added a requiremtn on python 2. (I think the result is probably correct but not deterministic). Commit: 9949053f430fcd44cdff6434f934146eecaa1d1f https://github.com/galaxyproject/galaxy/commit/9949053f430fcd44cdff6434f934… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_limit_to_species.py Log Message: ----------- Fix maf_limit_to_species.py if no species is given Commit: 2827dbf669ff2e9e2a7938aad0b81c94220c813d https://github.com/galaxyproject/galaxy/commit/2827dbf669ff2e9e2a7938aad0b8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_interval.py Log Message: ----------- Fix maf_to_interval.py Commit: 548b9c8c89121935e5557d98e6e8ec87327714bf https://github.com/galaxyproject/galaxy/commit/548b9c8c89121935e5557d98e6e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_bed.py Log Message: ----------- Fix maf_to_bed.py Commit: 2d36e8955e020958334088d6ba5853c1027d8b75 https://github.com/galaxyproject/galaxy/commit/2d36e8955e020958334088d6ba58… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix recursion issue in gff_filter_by_feature_count Commit: 918634f1fbbfafecbe9a25e869f82ea2df7e8edf https://github.com/galaxyproject/galaxy/commit/918634f1fbbfafecbe9a25e869f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Switch rpy2 to 2.9.4, 2.7.8 can't be resolved Commit: 491fe4251e97335505243f460f6a3bdf99df1556 https://github.com/galaxyproject/galaxy/commit/491fe4251e97335505243f460f6a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/uniq.xml Log Message: ----------- Fix uniq tests on OSX Commit: 77b43946f616b2e29b0550a21255a2c970dbd4dc https://github.com/galaxyproject/galaxy/commit/77b43946f616b2e29b0550a21255… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/next_gen_conversion/solid2fastq.xml Log Message: ----------- Fix solid2fastq tests Commit: 18ac62c1fd5952a94e5c6eaf4c3e357335a47ff2 https://github.com/galaxyproject/galaxy/commit/18ac62c1fd5952a94e5c6eaf4c3e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/wig_to_bigwig.xml Log Message: ----------- Fix wig_to_bigwig tool tests Commit: da4906dc56175cabd72a7d4b9b2ecce93bcad740 https://github.com/galaxyproject/galaxy/commit/da4906dc56175cabd72a7d4b9b2e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/functional/known_broken_tools.txt Log Message: ----------- Add GeneBed_Maf_Fasta2 to no test list Commit: c1dffec4ecdda1494a6169e3239c82dadbeda50c https://github.com/galaxyproject/galaxy/commit/c1dffec4ecdda1494a6169e3239c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/tailWrapper.xml Log Message: ----------- Quote tail wrapper inputs and outputs, drop interpreter attribute Commit: 05f18d029bb1308ab37e575f6972e8e18792e8b5 https://github.com/galaxyproject/galaxy/commit/05f18d029bb1308ab37e575f6972… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml Log Message: ----------- Fix linkToGProfile test Commit: 4acfd9a770518b33191a395dc1c606b82b67879a https://github.com/galaxyproject/galaxy/commit/4acfd9a770518b33191a395dc1c6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/sff_extractor.xml Log Message: ----------- Fix sffextractor tests by requiring python 2.7 Commit: f22f0ebb2f95415573a42c0b4a783dde8aeb8c04 https://github.com/galaxyproject/galaxy/commit/f22f0ebb2f95415573a42c0b4a78… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_split_by_species.xml Log Message: ----------- Sort maf_split_by_species test output Commit: e8d0ce39cf60b8311d9b749189a29025ad476144 https://github.com/galaxyproject/galaxy/commit/e8d0ce39cf60b8311d9b749189a2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml Log Message: ----------- Fix random order of fasta headers in maf_to_bed Commit: aee261daf7f87289063a91371fd66ffcb3c595b8 https://github.com/galaxyproject/galaxy/commit/aee261daf7f87289063a91371fd6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_fasta_multiple_sets.py Log Message: ----------- Fix random header order in MAF to FASTA Commit: 36196bd2be7b350c0aae85c44cd1fcb8a1b1c737 https://github.com/galaxyproject/galaxy/commit/36196bd2be7b350c0aae85c44cd1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_interval.xml Log Message: ----------- Specify maf ftype in maf_to_interval.xml Commit: 906951f28e075829444c8c222000e4af82a86ef9 https://github.com/galaxyproject/galaxy/commit/906951f28e075829444c8c222000… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/solid_tools/solid_qual_stats.xml Log Message: ----------- Single-quote paths in solid_qual_stats and fix test by using sim_size -- we have different float precision between py2 and py3. Commit: 72f95ba9c4bb940c892b8f6b37a1d91471d013c9 https://github.com/galaxyproject/galaxy/commit/72f95ba9c4bb940c892b8f6b37a1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/bed_to_bigbed.xml Log Message: ----------- Test bed_to_bigbed using compare="sim_size" Commit: 8b757f22d1489deb09a863cfc701f4ce1ea0c1f3 https://github.com/galaxyproject/galaxy/commit/8b757f22d1489deb09a863cfc701… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/functional/known_broken_tools.txt Log Message: ----------- Exclude bed_to_bigbed and wig_to_bigwig from tests They work, but required hg17.len to be present. Commit: 91b02cc6a80ea267743779ffcf4483ada5338cf9 https://github.com/galaxyproject/galaxy/commit/91b02cc6a80ea267743779ffcf44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh Log Message: ----------- Add .ci/jenkins/main* for testing tools in tool_conf.xml.main Commit: 7f220276cc2fb500447b0f320b3d4985855def01 https://github.com/galaxyproject/galaxy/commit/7f220276cc2fb500447b0f320b3d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/joinWrapper.py Log Message: ----------- py3: Fix comp1 tool Commit: c939e7bb616103fb4d79067cf3d8159e276524ea https://github.com/galaxyproject/galaxy/commit/c939e7bb616103fb4d79067cf3d8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Bump version of Summary Statistics for rpy2 version update Commit: 7f1f8a7a4eda4b753bcedcc25b11a9abe34175c6 https://github.com/galaxyproject/galaxy/commit/7f1f8a7a4eda4b753bcedcc25b11… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/ucsc.py M test/functional/known_broken_tools.txt M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/grouping.py M tools/stats/gsummary.xml Log Message: ----------- Merge pull request #6627 from mvdbeek/test_more_tools Test tools shipped with Galaxy Compare: https://github.com/galaxyproject/galaxy/compare/ae7b4fda8976...7f1f8a7a4eda **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9b488f: One last Selenium fix for collection interface cha...
by GitHub 05 Sep '18

05 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b488ff291a7d5c2204ed20b3f71769fe58d7e30 https://github.com/galaxyproject/galaxy/commit/9b488ff291a7d5c2204ed20b3f71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- One last Selenium fix for collection interface change. Commit: ae7b4fda89764ccae189141c75d1609a751b3add https://github.com/galaxyproject/galaxy/commit/ae7b4fda89764ccae189141c75d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #6672 from jmchilton/selenium_fixes_47 One last Selenium fix for collection interface change. Compare: https://github.com/galaxyproject/galaxy/compare/309c13b5ba42...ae7b4fda8976 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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