Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6d0b1492110d8758a34f412b881977480dd24ad https://github.com/galaxyproject/galaxy/commit/b6d0b1492110d8758a34f412b8819... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #5391 from dannon/release_17.09 [17.09] Constrain workflow tool panel entries to those not deleted. Commit: 889aa29d02aa54e04a1a31904f1b29b7453c49cf https://github.com/galaxyproject/galaxy/commit/889aa29d02aa54e04a1a31904f1b2... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda: pass subprocess arguments as list Commit: b8873c65ad8c2b14bf00de2330586e606c232787 https://github.com/galaxyproject/galaxy/commit/b8873c65ad8c2b14bf00de2330586... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Install the latest version of conda and conda-build Conda 4.3.33 contains a fix that should solve some conda env creation programs: https://github.com/conda/conda/pull/6766 Also support conda installation on x86 Linux architecture. Commit: 74d57cfc1c0d9d82b6893257438937ba0e37f5af https://github.com/galaxyproject/galaxy/commit/74d57cfc1c0d9d82b689325743893... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix subworkflow creation This fixes #5396. The problem was that we would override the content_id with an undefined value. Broken in https://github.com/galaxyproject/galaxy/pull/5249. Commit: f589a0cb5b45b5964e654fe7eb1602a13ac1bf57 https://github.com/galaxyproject/galaxy/commit/f589a0cb5b45b5964e654fe7eb160... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Build client Commit: d6fb37071dc4b425763c1e1aeb9b8d404cf111a0 https://github.com/galaxyproject/galaxy/commit/d6fb37071dc4b425763c1e1aeb9b8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #5398 from mvdbeek/subworkflow_creation_fix [17.09] Subworkflow creation fix Commit: b1c5186e1cb496facd4387bb569c231c0c434d13 https://github.com/galaxyproject/galaxy/commit/b1c5186e1cb496facd4387bb569c2... Author: John Chilton <jmchilton@gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5397 from nsoranzo/release_18.01_conda_fixes [18.01] Install latest conda and don't use shell=True Commit: 414c03124785f194bf46e84c95e20219423f4f16 https://github.com/galaxyproject/galaxy/commit/414c03124785f194bf46e84c95e20... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-29 (Mon, 29 Jan 2018) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Follow IUC and Drop r channel from default cond channels Commit: a70f2875b3b72d3cc50d41ea9120df8c3d03de32 https://github.com/galaxyproject/galaxy/commit/a70f2875b3b72d3cc50d41ea9120d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-29 (Mon, 29 Jan 2018) Changed paths: M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Remove r channel from more locations Commit: eb506b25b9cc02e828442ecb9772cc0d4bcc029b https://github.com/galaxyproject/galaxy/commit/eb506b25b9cc02e828442ecb9772c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-30 (Tue, 30 Jan 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml Log Message: ----------- Allow map-over when discovering dataset collections This would affect for example the mapping over of fastq-dump (and all other tools in the sra-toolkit). If one had attempted this previously the discovery phase would fail with: ``` galaxy.tools.parameters.output_collect ERROR 2018-01-30 08:56:46,369 Problem gathering output collection. Traceback (most recent call last): File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 169, in collect_dynamic_collections collection File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/managers/collections.py", line 216, in collection_builder_for return builder.BoundCollectionBuilder(dataset_collection, collection_type_description) File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/dataset_collections/builder.py", line 84, in __init__ raise Exception("Cannot reset elements of an already populated dataset collection.") Exception: Cannot reset elements of an already populated dataset collection. ``` Instead we force the collection state to be new when we are discovering output collection datasets, which seems reasonable to me. This includes an API testcase that would have failed previously. Commit: 9fcac13145854abf9445e3b75da3eee42c0d7383 https://github.com/galaxyproject/galaxy/commit/9fcac13145854abf9445e3b75da3e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-01-30 (Tue, 30 Jan 2018) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Fix the PJA type issue when mapping renames over nested lists. Commit: cad17b07c36ded48d3f1eaded98f0ea8e9dfd0c6 https://github.com/galaxyproject/galaxy/commit/cad17b07c36ded48d3f1eaded98f0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-30 (Tue, 30 Jan 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Revert "Revert extra assertions that are causing unrelated issues to surface." This reverts commit 4925660ab4aa2974c6ac8e94180180bac7db9781. Commit: 54e07568bef2687be10e317cd668d68ba68777bf https://github.com/galaxyproject/galaxy/commit/54e07568bef2687be10e317cd668d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-01-30 (Tue, 30 Jan 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/api/test_workflows.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml Log Message: ----------- Merge pull request #5413 from mvdbeek/fix_dynamic_collection_output_18_01 Allow map-over when discovering dataset collections Commit: 8e5d2d3214024d5cabf826c6389b6130dd30fd98 https://github.com/galaxyproject/galaxy/commit/8e5d2d3214024d5cabf826c6389b6... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #5414 from jmchilton/skip_invalid_pja [17.09] Fix the PJA type issue when mapping renames over nested lists. Commit: 34421966d41a9b9491d3388200c3642c8514b9f1 https://github.com/galaxyproject/galaxy/commit/34421966d41a9b9491d3388200c36... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #5406 from mvdbeek/conda_and_channel_order_update [17.05] Follow IUC and drop r channel from default conda channels Commit: c0c95548a3c77f361f09857e9d80a04a6b000e23 https://github.com/galaxyproject/galaxy/commit/c0c95548a3c77f361f09857e9d80a... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 5b23c0e87d2ed17075e6ba8d529da25f27dae8c8 https://github.com/galaxyproject/galaxy/commit/5b23c0e87d2ed17075e6ba8d529da... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M config/galaxy.yml.sample M doc/source/admin/dependency_resolvers.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Conflicts: client/galaxy/scripts/mvc/workflow/workflow-node.js config/galaxy.ini.sample static/maps/mvc/workflow/workflow-node.js.map static/scripts/mvc/workflow/workflow-node.js Commit: da002bdf44ff9c3809c15990e5f086d029c34533 https://github.com/galaxyproject/galaxy/commit/da002bdf44ff9c3809c15990e5f08... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M config/galaxy.yml.sample M doc/source/admin/dependency_resolvers.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/dataset_collections/structure.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools.py M test/api/test_workflows.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/28f5aca05695...da002bdf44ff