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

[galaxyproject/galaxy] 83ab84: change hicexplorer image name
by GitHub 11 Dec '17

11 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83ab849f3886e163ee4ab7267cc3949081994b57 https://github.com/galaxyproject/galaxy/commit/83ab849f3886e163ee4ab7267cc3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample Log Message: ----------- change hicexplorer image name Commit: 3d989243a9fb2228a434b729044b2428bd514cec https://github.com/galaxyproject/galaxy/commit/3d989243a9fb2228a434b729044b… Author: Enis Afgan <afgane(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample Log Message: ----------- Merge pull request #5177 from bgruening/hic_img_name change hicexplorer image name Compare: https://github.com/galaxyproject/galaxy/compare/477ab4eeb8c5...3d989243a9fb

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[galaxyproject/galaxy] f67682: don't copy subworkflows
by GitHub 11 Dec '17

11 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f676823c7a0e57d3346192eef935febde5a30e77 https://github.com/galaxyproject/galaxy/commit/f676823c7a0e57d3346192eef935… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/scripts/bundled/extended.bundled.js A static/scripts/libs/bibtex.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- don't copy subworkflows Commit: 477ab4eeb8c5feefd70dde96f7573750c08a1306 https://github.com/galaxyproject/galaxy/commit/477ab4eeb8c5feefd70dde96f757… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/scripts/bundled/extended.bundled.js A static/scripts/libs/bibtex.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #5185 from anatskiy/workflow_step_cloning_fix Don't clone subworkflows Compare: https://github.com/galaxyproject/galaxy/compare/e198dd75782c...477ab4eeb8c5

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[galaxyproject/galaxy] 3fa608: Use pysam.merge instead of samtools merge
by GitHub 10 Dec '17

10 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3fa608f54850d9a93e910cdc55fa1f87c4c87c7c https://github.com/galaxyproject/galaxy/commit/3fa608f54850d9a93e910cdc55fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Use pysam.merge instead of samtools merge Commit: 16d0d3ecafb47ca8f112e8fa339f492446f9e80c https://github.com/galaxyproject/galaxy/commit/16d0d3ecafb47ca8f112e8fa339f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A lib/galaxy/datatypes/test/1.unsorted.bam Log Message: ----------- Add unsorted test bam Commit: 3c9999d89acfdd7aa1f56969ca7e03da3d83e655 https://github.com/galaxyproject/galaxy/commit/3c9999d89acfdd7aa1f56969ca7e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/test/1.bam M lib/galaxy/datatypes/test/1.unsorted.bam Log Message: ----------- Use pysam for metadata setting and grooming There are also some noteworthy changes here: - We do always respect the sort-order specified in the header - If the sort order is not mentioned in the header or no header exists we coordinate-sort the file. - We do not use indexing to determine if a file is coordinate sorted, because this does not work reliably with samtools/pysam > 1.X, since arbitrarily sorted files can be indexed now. This also fixes advanced metadata setting (sort_order, bam_version and more), which appears to have been broken. This probably went by unnoticed because of the catch-all try-except-pass. The downside to fixing this is that I had to (temporarilly, hopefully) comment out the reference_names, reference_lengths, bam_header and readgroups attributes, because they led to the following error: ``` galaxy.model.metadata DEBUG 2017-11-19 14:47:30,540 loading metadata from file for: HistoryDatasetAssociation 582 galaxy.jobs.runners.local ERROR 2017-11-19 14:47:30,636 Job wrapper finish method failed Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/local.py", line 130, in queue_job job_wrapper.finish(stdout, stderr, exit_code) File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1357, in finish self.sa_session.flush() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 157, in do return getattr(self.registry(), name)(*args, **kwargs) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2019, in flush self._flush(objects) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2137, in _flush transaction.rollback(_capture_exception=True) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__ compat.reraise(exc_type, exc_value, exc_tb) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2101, in _flush flush_context.execute() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 373, in execute rec.execute(self) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 532, in execute uow File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 170, in save_obj mapper, table, update) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 706, in _emit_update_statements execute(statement, multiparams) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute return meth(self, multiparams, params) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement compiled_sql, distilled_params File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context context) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception exc_info File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context context) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute cursor.execute(statement, parameters) OperationalError: (psycopg2.OperationalError) index row size 7208 exceeds maximum 2712 for index "ix_history_dataset_association_metadata" HINT: Values larger than 1/3 of a buffer page cannot be indexed. Consider a function index of an MD5 hash of the value, or use full text indexing. [SQL: 'UPDATE history_dataset_association SET update_time=%(update_time)s, blurb=%(blurb)s, peek=%(peek)s, metadata=%(_metadata)s WHERE history_dataset_association.id = %(history_dataset_association_id)s'] [parameters: {'_metadata': <psycopg2.extensions.Binary object at 0x119ed8990>, 'update_time': datetime.datetime(2017, 11, 19, 13, 47, 30, 598058), 'history_dataset_association_id': 582, 'blurb': '3.5 KB', 'peek': 'Binary bam alignments file'}] ``` Commit: 369485a43ad50a877dc68324c1a2b6ab876030ea https://github.com/galaxyproject/galaxy/commit/369485a43ad50a877dc68324c1a2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py A test/unit/datatypes/test_bam.py Log Message: ----------- Move Bam doctests to unittests Commit: ae72e5668364f6f72861c21a62a641f9f65636e1 https://github.com/galaxyproject/galaxy/commit/ae72e5668364f6f72861c21a62a6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M test/unit/datatypes/test_bam.py Log Message: ----------- Use subprocess to check if pysam.index succeeds Checking if pysam.index succeeds tests whether a file is coordinate sorted. If pysam.index fails to index htslib writes to stderr and this fails set meta tool. To prevent this we run this in a subprocess and discard stderr. Commit: 836aea072e84411fb4a24e37fb306b5ec72044c6 https://github.com/galaxyproject/galaxy/commit/836aea072e84411fb4a24e37fb30… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A lib/galaxy/datatypes/test/2.shuffled.bam Log Message: ----------- Add test file with random order Commit: bac56d6b27068d3744e84eb9756bc28bf392f718 https://github.com/galaxyproject/galaxy/commit/bac56d6b27068d3744e84eb9756b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml M tools/data_source/upload.xml Log Message: ----------- Drop samtools from metadata and upload tools We only need samtools for the dataproviders, which shouldn't be used by these tools. Commit: df35d089e3ea8c15330afaeedfa24e9c2f0fa7b2 https://github.com/galaxyproject/galaxy/commit/df35d089e3ea8c15330afaeedfa2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram M test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py Log Message: ----------- Add more unittests for CRAM, bcf and vcf Commit: 3f6a59e85ff8acf2fb0b39670f450a523ea11f38 https://github.com/galaxyproject/galaxy/commit/3f6a59e85ff8acf2fb0b39670f45… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Replace bcftools index with pysam.bcftools.index or pysam.tabix_index Commit: 8e580ec7ac599993ae082732b5c80f2b9bcce493 https://github.com/galaxyproject/galaxy/commit/8e580ec7ac599993ae082732b5c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Metadata fixes for VcfGz Commit: 0ac77ad7fd5c6d6660521d69f6010cb61d4947ac https://github.com/galaxyproject/galaxy/commit/0ac77ad7fd5c6d6660521d69f601… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/unit/datatypes/test_vcf.py M test/unit/datatypes/util.py Log Message: ----------- Fix Vcf index generation and test Commit: 6ca896ff9b199ac097f408e35e37a3365ff2ec46 https://github.com/galaxyproject/galaxy/commit/6ca896ff9b199ac097f408e35e37… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/unit/datatypes/test_bcf.py M test/unit/datatypes/test_cram.py M test/unit/datatypes/test_vcf.py M test/unit/datatypes/util.py Log Message: ----------- Fix index file syntax and fix linting problems Commit: 9c4a2f70ea6a62f35b3c736730fcc71bddf6dce9 https://github.com/galaxyproject/galaxy/commit/9c4a2f70ea6a62f35b3c736730fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py Log Message: ----------- Tabix indexing fixes. Upstream used 'index' instead of 'index_filename', and 'force' is now required since we precreate the destination location. Commit: 2a6e00dd001ea4f27cd7d9a12cddfcf9649da7ef https://github.com/galaxyproject/galaxy/commit/2a6e00dd001ea4f27cd7d9a12cdd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M test/unit/datatypes/test_cram.py Log Message: ----------- one more linting fix Commit: 07158e03308e026ee013bd6a50708167918c2d27 https://github.com/galaxyproject/galaxy/commit/07158e03308e026ee013bd6a5070… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Need force=True in pysam.tabix_index because the index file path exists in the object store Commit: 64deb4f935ac7969a0e81024297d84d9831a8cfd https://github.com/galaxyproject/galaxy/commit/64deb4f935ac7969a0e81024297d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/converters/cram_to_bam.py Log Message: ----------- We can use multiple threads when converting cram to bam files Commit: 90a56aea3f19df6943dfc648474d161e5c8f6d66 https://github.com/galaxyproject/galaxy/commit/90a56aea3f19df6943dfc648474d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Use more threads when sorting BAM files and GALAXY_SLOTS is set Commit: eb636c11361ef8f6cf85c8750f0a37608dcbee1a https://github.com/galaxyproject/galaxy/commit/eb636c11361ef8f6cf85c8750f0a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/util.py Log Message: ----------- Make sure files don't change in-place Commit: 1195183ea63c3916e1b8e163b2cc0839bd18d8c4 https://github.com/galaxyproject/galaxy/commit/1195183ea63c3916e1b8e163b2cc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Symlink tbi index to work around pysam limitation Before https://github.com/pysam-developers/pysam/pull/586 is merged and a new release is out we create a symlink to the tbi file, which is required for creating TabixFile instances. Since we want to cleanup the symlinks I turned `get_data_file` into a contextmanager. Along the way I also changed many open()/close() calls to `with` statements. Commit: 4795e490636e9a9234cb2d61c0a14508472a297d https://github.com/galaxyproject/galaxy/commit/4795e490636e9a9234cb2d61c0a1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Detect if index symlink hack is necessary Commit: 46371d1251ed80b740956dc7111708aa93041092 https://github.com/galaxyproject/galaxy/commit/46371d1251ed80b740956dc71117… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M test/unit/datatypes/converters/test_interval_to_tabix.py M test/unit/datatypes/util.py Log Message: ----------- Decompose interval_to_tabix converter script This renames some variables to make it clearer what files they reflect. Also adds a very basic test that this works as intended. Commit: 309b71720e3b5615fac6abd028aa66735fa94eef https://github.com/galaxyproject/galaxy/commit/309b71720e3b5615fac6abd028aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py R lib/galaxy/datatypes/test/1.unsorted.bam M lib/galaxy/visualization/data_providers/genome.py M test/unit/datatypes/util.py Log Message: ----------- Improvements to datatypes suggested by @nsoranzo Commit: e198dd75782ce5b2a9619a5283e77a026393e149 https://github.com/galaxyproject/galaxy/commit/e198dd75782ce5b2a9619a5283e7… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam M lib/galaxy/visualization/data_providers/genome.py A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #5037 from mvdbeek/samtools_to_pysam Samtools to pysam Compare: https://github.com/galaxyproject/galaxy/compare/5ad4f57a63b0...e198dd75782c

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[galaxyproject/galaxy] 4b0a4d: Another fix for 404 on /workflow.
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b0a4d3d7d44fa6efd416ee168e484ba8da50dab https://github.com/galaxyproject/galaxy/commit/4b0a4d3d7d44fa6efd416ee168e4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Another fix for 404 on /workflow. Similar to 82f44479fcc92fae0507c50aad19b2f2776ccadc. Commit: 5ad4f57a63b00cf6f27a6852e13d87d7902cac4a https://github.com/galaxyproject/galaxy/commit/5ad4f57a63b00cf6f27a6852e13d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #5170 from jmchilton/workflow_list Another fix for 404 on /workflow. Compare: https://github.com/galaxyproject/galaxy/compare/b99180c5a23c...5ad4f57a63b0

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[galaxyproject/galaxy] 5602f9: Fix inputFilled logic in workflow editor w/ collec...
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5602f911e757e2c08485166e61c39d7c854a7446 https://github.com/galaxyproject/galaxy/commit/5602f911e757e2c08485166e61c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix inputFilled logic in workflow editor w/ collections. Commit: 30bada4c4a96eeb78a43aefa85a48fbcb6966eeb https://github.com/galaxyproject/galaxy/commit/30bada4c4a96eeb78a43aefa85a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix another undefined collection type var. Commit: d3d6658160684211fda02c92ed1fb54d018a7471 https://github.com/galaxyproject/galaxy/commit/d3d6658160684211fda02c92ed1f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Some misc cleanup in workflow-terminals.js Commit: 7a1e8c67627866b431917ecee0f974e9a0cdc418 https://github.com/galaxyproject/galaxy/commit/7a1e8c67627866b431917ecee0f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Client formatting. Commit: fd3a558895feeea9e50835e3ddfbcf88a38db40e https://github.com/galaxyproject/galaxy/commit/fd3a558895feeea9e50835e3ddfb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Client build. Commit: b99180c5a23cd7477b5a630a7a6d7ee994b67b9a https://github.com/galaxyproject/galaxy/commit/b99180c5a23cd7477b5a630a7a6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #5166 from dannon/fix_workflow_collections Fix workflow collection attachments Compare: https://github.com/galaxyproject/galaxy/compare/db317b6341e9...b99180c5a23c

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[galaxyproject/galaxy] e8a128: [17.09] Deployer doc fixes.
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: e8a1280f78e1fa19e2173f922f2221ea28279964 https://github.com/galaxyproject/galaxy/commit/e8a1280f78e1fa19e2173f922f22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- [17.09] Deployer doc fixes. Commit: 42c572f34469ec39a55588504a97f1466c59f332 https://github.com/galaxyproject/galaxy/commit/42c572f34469ec39a55588504a97… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- Merge pull request #5147 from jmchilton/1709_docs_fixes [17.09] Small deployer doc fixes. Compare: https://github.com/galaxyproject/galaxy/compare/e9f05cb1b11d...42c572f34469

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[galaxyproject/galaxy] 82f444: Resolve broken link in for all workflows
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82f44479fcc92fae0507c50aad19b2f2776ccadc https://github.com/galaxyproject/galaxy/commit/82f44479fcc92fae0507c50aad19… Author: Milad Miladi <mmiladi(a)users.noreply.github.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Resolve broken link in for all workflows The docker galaxy flavors built on dev branch have a broken link in tool panel, href in "All workflows" section. This should fix it. Commit: eab3c32cfad9b3acebeceb56e3d948320558d0b9 https://github.com/galaxyproject/galaxy/commit/eab3c32cfad9b3acebeceb56e3d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Merge branch 'toolpanel-fixlink' into dev Commit: db317b6341e9267371a048131fb95a9387c31842 https://github.com/galaxyproject/galaxy/commit/db317b6341e9267371a048131fb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Client build w/ merge of mmiladi:toolpanel-fixlink Compare: https://github.com/galaxyproject/galaxy/compare/044dcfbb216a...db317b6341e9

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[galaxyproject/galaxy] 3dcf95: Test resubmit for completely dynamic JobDestinatio...
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3dcf9549f6bb4a3d0a5420185c2e7dedb78cc4d5 https://github.com/galaxyproject/galaxy/commit/3dcf9549f6bb4a3d0a5420185c2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py Log Message: ----------- Test resubmit for completely dynamic JobDestination structures. Commit: 044dcfbb216ad1b2fb46933c6b21597828e42a91 https://github.com/galaxyproject/galaxy/commit/044dcfbb216ad1b2fb46933c6b21… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py Log Message: ----------- Merge pull request #5139 from jmchilton/resubmit_dynamic Test resubmit for dynamic JobDestination structures. Compare: https://github.com/galaxyproject/galaxy/compare/fe0fdeb4ce35...044dcfbb216a

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[galaxyproject/galaxy] 3dfbbc: Provide Galaxy.config var to indicate whether onlo...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3dfbbc7e081cae0c8b95b727e3791915afcc47ec https://github.com/galaxyproject/galaxy/commit/3dfbbc7e081cae0c8b95b727e379… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/onload.js M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Provide Galaxy.config var to indicate whether onload webhooks should kick off; use it. Fixes shed/reports use of them. Commit: 6f80bed294e99abbc5f880ea7ee0b781e60f7e2a https://github.com/galaxyproject/galaxy/commit/6f80bed294e99abbc5f880ea7ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Minor onload.js cleanup. Commit: 7f1b77ff16c2678327130f3d7282cd900130def8 https://github.com/galaxyproject/galaxy/commit/7f1b77ff16c2678327130f3d7282… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js Log Message: ----------- Move tours kicker out of onload.js; just use the import. Commit: 8858b5511cdaf282eb5a1e75eda42ce7dde25b42 https://github.com/galaxyproject/galaxy/commit/8858b5511cdaf282eb5a1e75eda4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Standardize import naming a little. Commit: d87e5755c73c59c3dfc4291b76da059fe8a81675 https://github.com/galaxyproject/galaxy/commit/d87e5755c73c59c3dfc4291b76da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Tours import/export cleanup. tour_opts is internal only. Commit: 3f5aabbf150bd126b8bfa209214874a42399c666 https://github.com/galaxyproject/galaxy/commit/3f5aabbf150bd126b8bfa2092148… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Tour launching refactoring. Commit: a2cf121e34dc4cdb556ffb47337199d1e8a15f1b https://github.com/galaxyproject/galaxy/commit/a2cf121e34dc4cdb556ffb473371… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Reduce tour launch duplication, refine module interface. Commit: d68dd305d86ae5767b00a0dbd7b2736101500e0a https://github.com/galaxyproject/galaxy/commit/d68dd305d86ae5767b00a0dbd7b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Run client-format. Commit: 03062992cfe037ea6d190c8587de39e66070fc55 https://github.com/galaxyproject/galaxy/commit/03062992cfe037ea6d190c8587de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Actually add /config to the commit... Commit: afae7c5dbd05bd4e69f4278902b8a0d1e3fde900 https://github.com/galaxyproject/galaxy/commit/afae7c5dbd05bd4e69f4278902b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Slight reorg in tours.js; internal stuff first, exports at the end. Commit: 2a7daaaefb605e7567cdafb71d49903e3db3389d https://github.com/galaxyproject/galaxy/commit/2a7daaaefb605e7567cdafb71d49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Rebuild client. Commit: fe0fdeb4ce35dc1de9fa2ce26ffffab6276552e0 https://github.com/galaxyproject/galaxy/commit/fe0fdeb4ce35dc1de9fa2ce26fff… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Merge pull request #5116 from dannon/onload_webhook_segmentation Onload webhook toggles. Compare: https://github.com/galaxyproject/galaxy/compare/30196f5941df...fe0fdeb4ce35

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[galaxyproject/galaxy] 688128: Minor tweak; use dot notation in history-list.js
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 688128feed6147e359969f19775630d11a5281c1 https://github.com/galaxyproject/galaxy/commit/688128feed6147e359969f197756… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Minor tweak; use dot notation in history-list.js Commit: 12da37bb9ab1fbf35b13a36ba808d23f054a738c https://github.com/galaxyproject/galaxy/commit/12da37bb9ab1fbf35b13a36ba808… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Grid-view cleanup. Commit: 35d854b8c13d951692e9f0bc9564031d1dc790e0 https://github.com/galaxyproject/galaxy/commit/35d854b8c13d951692e9f0bc9564… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Fixes in grid-template. A couple redefined vars, one used out of scope, and some general cleanup. Commit: f296d1f3334098481f56ac82ea861554cb48ab38 https://github.com/galaxyproject/galaxy/commit/f296d1f3334098481f56ac82ea86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Minor formatting. Commit: 53bcd063bce83257546a46918d73074491693324 https://github.com/galaxyproject/galaxy/commit/53bcd063bce83257546a46918d73… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Started refactoring more dramatically, but I think we probably want to do a bigger rewrite of this stuff with Vue grid components, Vuex, etc., so this simple subclassing should fix the problems we're seeing for now. Commit: cb6bbe3a0fbf5fb12507ddc391366b24177724c0 https://github.com/galaxyproject/galaxy/commit/cb6bbe3a0fbf5fb12507ddc39136… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Client format. Commit: 556c17d154e2efe496484b917f25acacaaba7c87 https://github.com/galaxyproject/galaxy/commit/556c17d154e2efe496484b917f25… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Convert a bunch of iterables to use 'of' syntax instead of 'in'. Commit: eca993539a2e00895e32316e939e09fdfb79b84d https://github.com/galaxyproject/galaxy/commit/eca993539a2e00895e32316e939e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.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-repeat.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.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/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M 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/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/repositories.py A lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.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/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M test/api/test_workflows.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/tools/test_tool_validation.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fix-history-copy Commit: a92da1c109c3e5cbc530d17cd148a5877098a676 https://github.com/galaxyproject/galaxy/commit/a92da1c109c3e5cbc530d17cd148… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- use encoded ids for popup anchor identifiers instead of sequence; this is more robust Commit: e08a3d0ffd01a7d58ad7445ef19050e6fbbefae3 https://github.com/galaxyproject/galaxy/commit/e08a3d0ffd01a7d58ad7445ef190… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js Log Message: ----------- Make client Commit: 30196f5941df704f6bb0a2a215315db08ffc92bf https://github.com/galaxyproject/galaxy/commit/30196f5941df704f6bb0a2a21531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js Log Message: ----------- Merge pull request #5144 from dannon/fix-history-copy Fix history copy Compare: https://github.com/galaxyproject/galaxy/compare/ef13e2857851...30196f5941df

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