Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8affe206df782658dbc388d5ffe1c5c1d6a136ef https://github.com/galaxyproject/galaxy/commit/8affe206df782658dbc388d5ffe1c... Author: mvdbeek <m.vandenbeek@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/df5cab38ae35a38e1d7486d8c2fc0... Author: mvdbeek <m.vandenbeek@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/6352a0ef3ea5d80771276bcf4b928... Author: mvdbeek <m.vandenbeek@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/36c74bbafa972f0e76ad8bf7befa2... Author: mvdbeek <m.vandenbeek@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/6c7203b83d19d1f79bd6b1790ce24... Author: mvdbeek <m.vandenbeek@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/6405aeb86c2240e010fadcd4e4758... Author: mvdbeek <m.vandenbeek@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/8190c3fc4389299c8d9484bf3b340... Author: mvdbeek <m.vandenbeek@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/3fcf1e336dd2e32b0199388528078... Author: mvdbeek <m.vandenbeek@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/2d732715ff50241fcddfab5879530... Author: mvdbeek <m.vandenbeek@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/8889bd0a3d93266893a21dedefa9f... Author: mvdbeek <m.vandenbeek@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/9949053f430fcd44cdff6434f9341... Author: mvdbeek <m.vandenbeek@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/2827dbf669ff2e9e2a7938aad0b81... Author: mvdbeek <m.vandenbeek@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/548b9c8c89121935e5557d98e6e8e... Author: mvdbeek <m.vandenbeek@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/2d36e8955e020958334088d6ba585... Author: mvdbeek <m.vandenbeek@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/918634f1fbbfafecbe9a25e869f82... Author: mvdbeek <m.vandenbeek@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/491fe4251e97335505243f460f6a3... Author: mvdbeek <m.vandenbeek@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/77b43946f616b2e29b0550a21255a... Author: mvdbeek <m.vandenbeek@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/18ac62c1fd5952a94e5c6eaf4c3e3... Author: mvdbeek <m.vandenbeek@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/da4906dc56175cabd72a7d4b9b2ec... Author: mvdbeek <m.vandenbeek@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/c1dffec4ecdda1494a6169e3239c8... Author: mvdbeek <m.vandenbeek@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/05f18d029bb1308ab37e575f6972e... Author: mvdbeek <m.vandenbeek@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/4acfd9a770518b33191a395dc1c60... Author: mvdbeek <m.vandenbeek@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/f22f0ebb2f95415573a42c0b4a783... Author: mvdbeek <m.vandenbeek@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/e8d0ce39cf60b8311d9b749189a29... Author: mvdbeek <m.vandenbeek@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/aee261daf7f87289063a91371fd66... Author: mvdbeek <m.vandenbeek@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/36196bd2be7b350c0aae85c44cd1f... Author: mvdbeek <m.vandenbeek@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/906951f28e075829444c8c222000e... Author: mvdbeek <m.vandenbeek@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/72f95ba9c4bb940c892b8f6b37a1d... Author: mvdbeek <m.vandenbeek@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/8b757f22d1489deb09a863cfc701f... Author: mvdbeek <m.vandenbeek@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/91b02cc6a80ea267743779ffcf448... Author: mvdbeek <m.vandenbeek@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/7f220276cc2fb500447b0f320b3d4... Author: mvdbeek <m.vandenbeek@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/c939e7bb616103fb4d79067cf3d81... Author: mvdbeek <m.vandenbeek@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/7f1f8a7a4eda4b753bcedcc25b11a... Author: John Chilton <jmchilton@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.