- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 03b59a: Committing format changes to the user impersonatio...
by GitHub 13 Jul '16

13 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03b59aacc33837f8160ecd45869d7f4df67fc6c6 https://github.com/galaxyproject/galaxy/commit/03b59aacc33837f8160ecd45869d… Author: galaxy <galaxy(a)galaxy.development> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M templates/admin/impersonate.mako Log Message: ----------- Committing format changes to the user impersonation dropdown. Commit: 7bbe0a2171232d6c7f04c57d045a9cce19b29476 https://github.com/galaxyproject/galaxy/commit/7bbe0a2171232d6c7f04c57d045a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M templates/admin/impersonate.mako Log Message: ----------- Merge pull request #2612 from sszakony/dev Committing format changes to the user impersonation dropdown. Compare: https://github.com/galaxyproject/galaxy/compare/f3e9736ca3a5...7bbe0a217123

1 0

[galaxyproject/usegalaxy-playbook] a5cccb: Update Test
by GitHub 11 Jul '16

11 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a5cccbe1c250a70d005754e2bb28c54cc714e650 https://github.com/galaxyproject/usegalaxy-playbook/commit/a5cccbe1c250a70d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update Test

1 0

[galaxyproject/galaxy] ca82e6: Deletes existing jobs with same ID when re-submitt...
by GitHub 11 Jul '16

11 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca82e6d746a685209b9585b3f69128a55198f801 https://github.com/galaxyproject/galaxy/commit/ca82e6d746a685209b9585b3f691… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Deletes existing jobs with same ID when re-submitting. Commit: 01fd25b9f4b79b4f2868efc51ad76e19fc132b5d https://github.com/galaxyproject/galaxy/commit/01fd25b9f4b79b4f2868efc51ad7… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Changes use of produce_unique_k8s_job_name to be able to use both job and job_wrappers. Commit: 409eb373cd9233f7925c64e9c5716859a2363ba1 https://github.com/galaxyproject/galaxy/commit/409eb373cd9233f7925c64e9c571… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Fixes stop job method so that it correctly scales down the Kubernetes job. Commit: 65a937965a22c46922f9b731475561e38809e588 https://github.com/galaxyproject/galaxy/commit/65a937965a22c46922f9b7314755… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improves handling of Kubernetes logs Commit: e8bf2df21fe7fb7405ea283a41eae22e6d58509f https://github.com/galaxyproject/galaxy/commit/e8bf2df21fe7fb7405ea283a41ea… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Corrects usage of pods retrials parameters set in runner and container destinations. Commit: 89b5f3f47f14fa82065b83326332313ec8cca629 https://github.com/galaxyproject/galaxy/commit/89b5f3f47f14fa82065b83326332… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Uses exception instead of pykube.exceptions.HTTPError to manage missing pod's log exception. Commit: 9db3453e6559cb883af22793b741a84f3abd071c https://github.com/galaxyproject/galaxy/commit/9db3453e6559cb883af22793b741… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Overrides parent fail_job to save stdout/stderr of pods when Kubernetes job fails (otherwise lost). Commit: 5eb60b3448f2cdf8706aa2ab43e4d51dcfc0a0cb https://github.com/galaxyproject/galaxy/commit/5eb60b3448f2cdf8706aa2ab43e4… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds missing whitespace to line in Kubernetes runner. Commit: f3e9736ca3a592d9aed006ecfd072f67cebfa006 https://github.com/galaxyproject/galaxy/commit/f3e9736ca3a592d9aed006ecfd07… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #2559 from phnmnl/feature/failingPodsNotDetected Kubernetes runner: improves handling of failed jobs Compare: https://github.com/galaxyproject/galaxy/compare/a74a23764cc1...f3e9736ca3a5

1 0

[galaxyproject/galaxy] 4ea881: Fix old bug in non-allowed_images.yml GIEs
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4ea881caa21602c5562224fa268ff87788eee0dd https://github.com/galaxyproject/galaxy/commit/4ea881caa21602c5562224fa268f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix old bug in non-allowed_images.yml GIEs Commit: 1069a69ae08a4a2db609aebb03c4a8fa53162777 https://github.com/galaxyproject/galaxy/commit/1069a69ae08a4a2db609aebb03c4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2550 from erasche/asdf [16.04] Fix old bug in non-allowed_images.yml GIEs Commit: c3bf89f75093bfe73f09d0f33dff8df6d60f9269 https://github.com/galaxyproject/galaxy/commit/c3bf89f75093bfe73f09d0f33dff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Fix tag_autocomplete issue. When we swapped to tag manager the signature changed and some of these were missed. Commit: 1507bd37fe8cb872975e46a6e7be468e984db0d8 https://github.com/galaxyproject/galaxy/commit/1507bd37fe8cb872975e46a6e7be… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- More defensive proxying Commit: f8e40bb5951cc38dce118cebcc09a5cc3ca96930 https://github.com/galaxyproject/galaxy/commit/f8e40bb5951cc38dce118cebcc09… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge pull request #2585 from erasche/backport-proxy-fix [16.04] Backport proxy fixes Commit: 7c2c2ca62a069700725c67e08053389b583680e7 https://github.com/galaxyproject/galaxy/commit/7c2c2ca62a069700725c67e08053… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Tabular dataset chunking fix which should prevent duplicated lines. Skipping to the newline previously shifted the chunk past where it should read. Commit: acdfd2423f3e8764375d0b7a23dad3c919db47fc https://github.com/galaxyproject/galaxy/commit/acdfd2423f3e8764375d0b7a23da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Rename vars to be sensible, add comment to clarify what this is doing. Commit: 84d152082009418f2fd5dfe0e9001e8924a678fc https://github.com/galaxyproject/galaxy/commit/84d152082009418f2fd5dfe0e900… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Absolute positioning for tabular dataset chunking, vs abstract chunk. Ships a minimum of one line regardless of size, and relies on client to know position. Commit: ca4b51b390d14077188b5226e4c83ed0991dcbb5 https://github.com/galaxyproject/galaxy/commit/ca4b51b390d14077188b5226e4c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Make client with new tabular display. Commit: a65faa961ca434901baaaeffe2e5926d4ac523c1 https://github.com/galaxyproject/galaxy/commit/a65faa961ca434901baaaeffe2e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix tabular chunked display offset=0 request, pass through ck_size to allow client specification of chunk size overriding the app defaults (neither of these are used by the js client currently though) Commit: d7cdf74bdf2690ab1d83cb262021251ae3e28d14 https://github.com/galaxyproject/galaxy/commit/d7cdf74bdf2690ab1d83cb262021… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Handle the case when the last character of the initial read is a newline. Commit: b7718a0f9ae3a626ab88080e0798a451597984c8 https://github.com/galaxyproject/galaxy/commit/b7718a0f9ae3a626ab88080e0798… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Swap ck_size default from 0 to None to indicate unset. This does not change any behavior at all, but @nsoranzo requested the change to make usage more clear. Commit: 1d8f39d987217c09048e05e1d5443173eb02a9f2 https://github.com/galaxyproject/galaxy/commit/1d8f39d987217c09048e05e1d544… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove old, unused arguments from some display_dataset methods, minor argument tweaks. Commit: 4da2119c2560c68cb716270933959eb8cf3d48ed https://github.com/galaxyproject/galaxy/commit/4da2119c2560c68cb71627093395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Remove explicit 'chunk' parameter passthrough in datasets API Commit: ab2e48bae7395661ce1112363fe167968582e919 https://github.com/galaxyproject/galaxy/commit/ab2e48bae7395661ce1112363fe1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Merge pull request #2569 from dannon/workflow_tag_fixes [16.04] Fix tag_autocomplete issue in workflow editor. Commit: 05c063b13a3fb4acf99af4ecbeb5d2350369301d https://github.com/galaxyproject/galaxy/commit/05c063b13a3fb4acf99af4ecbeb5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Merge pull request #2587 from dannon/backport_tabular_fix [16.04] Tabular Dataset Display Fixes Commit: a74a23764cc1aa0a481d0e2ea65ac26a8f151865 https://github.com/galaxyproject/galaxy/commit/a74a23764cc1aa0a481d0e2ea65a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/77f547ed89a9...a74a23764cc1

1 0

[galaxyproject/galaxy] 7c2c2c: Tabular dataset chunking fix which should prevent ...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 7c2c2ca62a069700725c67e08053389b583680e7 https://github.com/galaxyproject/galaxy/commit/7c2c2ca62a069700725c67e08053… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Tabular dataset chunking fix which should prevent duplicated lines. Skipping to the newline previously shifted the chunk past where it should read. Commit: acdfd2423f3e8764375d0b7a23dad3c919db47fc https://github.com/galaxyproject/galaxy/commit/acdfd2423f3e8764375d0b7a23da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Rename vars to be sensible, add comment to clarify what this is doing. Commit: 84d152082009418f2fd5dfe0e9001e8924a678fc https://github.com/galaxyproject/galaxy/commit/84d152082009418f2fd5dfe0e900… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Absolute positioning for tabular dataset chunking, vs abstract chunk. Ships a minimum of one line regardless of size, and relies on client to know position. Commit: ca4b51b390d14077188b5226e4c83ed0991dcbb5 https://github.com/galaxyproject/galaxy/commit/ca4b51b390d14077188b5226e4c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Make client with new tabular display. Commit: a65faa961ca434901baaaeffe2e5926d4ac523c1 https://github.com/galaxyproject/galaxy/commit/a65faa961ca434901baaaeffe2e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix tabular chunked display offset=0 request, pass through ck_size to allow client specification of chunk size overriding the app defaults (neither of these are used by the js client currently though) Commit: d7cdf74bdf2690ab1d83cb262021251ae3e28d14 https://github.com/galaxyproject/galaxy/commit/d7cdf74bdf2690ab1d83cb262021… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Handle the case when the last character of the initial read is a newline. Commit: b7718a0f9ae3a626ab88080e0798a451597984c8 https://github.com/galaxyproject/galaxy/commit/b7718a0f9ae3a626ab88080e0798… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Swap ck_size default from 0 to None to indicate unset. This does not change any behavior at all, but @nsoranzo requested the change to make usage more clear. Commit: 1d8f39d987217c09048e05e1d5443173eb02a9f2 https://github.com/galaxyproject/galaxy/commit/1d8f39d987217c09048e05e1d544… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove old, unused arguments from some display_dataset methods, minor argument tweaks. Commit: 4da2119c2560c68cb716270933959eb8cf3d48ed https://github.com/galaxyproject/galaxy/commit/4da2119c2560c68cb71627093395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Remove explicit 'chunk' parameter passthrough in datasets API Commit: 05c063b13a3fb4acf99af4ecbeb5d2350369301d https://github.com/galaxyproject/galaxy/commit/05c063b13a3fb4acf99af4ecbeb5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/data.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/dataset/data.js Log Message: ----------- Merge pull request #2587 from dannon/backport_tabular_fix [16.04] Tabular Dataset Display Fixes Compare: https://github.com/galaxyproject/galaxy/compare/ab2e48bae739...05c063b13a3f

1 0

[galaxyproject/galaxy] 61a113: When CONDA_ALREADY_INSTALLED is undefined there's ...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61a11341f9eb5f18ac33bd88e6acefc37a6f46af https://github.com/galaxyproject/galaxy/commit/61a11341f9eb5f18ac33bd88e6ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- When CONDA_ALREADY_INSTALLED is undefined there's an error due to the number of arguments in the boolean expression (we actually *do* always want a 1 or 0 there, never empty) Commit: 77f547ed89a90e31df6e388e311bef29d18f2e65 https://github.com/galaxyproject/galaxy/commit/77f547ed89a90e31df6e388e311b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2599 from dannon/fix_startup_condaskip When CONDA_ALREADY_INSTALLED is undefined there's an error due to the… Compare: https://github.com/galaxyproject/galaxy/compare/c0101e011fc3...77f547ed89a9

1 0

[galaxyproject/galaxy] c3bf89: Fix tag_autocomplete issue. When we swapped to ta...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: c3bf89f75093bfe73f09d0f33dff8df6d60f9269 https://github.com/galaxyproject/galaxy/commit/c3bf89f75093bfe73f09d0f33dff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Fix tag_autocomplete issue. When we swapped to tag manager the signature changed and some of these were missed. Commit: ab2e48bae7395661ce1112363fe167968582e919 https://github.com/galaxyproject/galaxy/commit/ab2e48bae7395661ce1112363fe1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Merge pull request #2569 from dannon/workflow_tag_fixes [16.04] Fix tag_autocomplete issue in workflow editor. Compare: https://github.com/galaxyproject/galaxy/compare/f8e40bb5951c...ab2e48bae739

1 0

[galaxyproject/galaxy] b53a92: Add Warning when Conda is installed because we ski...
by GitHub 08 Jul '16

08 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b53a9275d54d8ed0373a11a4e95c500619a3d5b0 https://github.com/galaxyproject/galaxy/commit/b53a9275d54d8ed0373a11a4e95c… Author: remimarenco <remi.marenco(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Add Warning when Conda is installed because we skip the virtualenv creation Fix the case where we could have conda not installed but not setting VirtualEnv still (and have this non relevant warning Commit: de702db55d8f1ca397b4ab926085e006cd39a490 https://github.com/galaxyproject/galaxy/commit/de702db55d8f1ca397b4ab926085… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- s/creation/activation. Thx @nsoranzo Commit: c0101e011fc3aacad1533d1bb80fdf4588c6bdb6 https://github.com/galaxyproject/galaxy/commit/c0101e011fc3aacad1533d1bb80f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2596 from remimarenco/conda_virtualenv_warning Add Warning when Conda is installed Compare: https://github.com/galaxyproject/galaxy/compare/83f1b07687a5...c0101e011fc3

1 0

[galaxyproject/galaxy] 89b838: Add controller consistent workflow api endpoint
by GitHub 07 Jul '16

07 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89b83885a79c58e28b305450ca33e08343d421cb https://github.com/galaxyproject/galaxy/commit/89b83885a79c58e28b305450ca33… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js Log Message: ----------- Add controller consistent workflow api endpoint Commit: 83f1b07687a5397bec60d4d57a2e0c9bcb44deda https://github.com/galaxyproject/galaxy/commit/83f1b07687a5397bec60d4d57a2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js Log Message: ----------- Merge pull request #2077 from guerler/revise_workflow_run_004 Run workflow form revision Compare: https://github.com/galaxyproject/galaxy/compare/834c97a81da6...83f1b07687a5

1 0

[galaxyproject/galaxy] a074af: Ignore W503 as PEP 8 has reversed its position on ...
by GitHub 07 Jul '16

07 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a074af5668bc37685649a245e48f2f6e60613591 https://github.com/galaxyproject/galaxy/commit/a074af5668bc37685649a245e48f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M setup.cfg Log Message: ----------- Ignore W503 as PEP 8 has reversed its position on this. Commit: 834c97a81da6cef6cfab0a14e86318fcc7cb38fe https://github.com/galaxyproject/galaxy/commit/834c97a81da6cef6cfab0a14e863… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M setup.cfg Log Message: ----------- Merge pull request #2594 from natefoo/ignore-w503 Ignore W503 (line break before binary operator) as PEP 8 has reversed its position on this. Compare: https://github.com/galaxyproject/galaxy/compare/05eebac85ded...834c97a81da6

1 0