galaxy-commits November 2016

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] 6c4d43: Add note about building docs to Makefile.
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c4d430d75781dac112f0c7b56fe61208d081f1c https://github.com/galaxyproject/galaxy/commit/6c4d430d75781dac112f0c7b56fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M Makefile Log Message: ----------- Add note about building docs to Makefile. Commit: 66cc4c3bbe4a90cd68d935574691c31b8053804e https://github.com/galaxyproject/galaxy/commit/66cc4c3bbe4a90cd68d935574691… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #3167 from jmchilton/doc_note Add note about building docs to Makefile. Compare: https://github.com/galaxyproject/galaxy/compare/ca4e8914ecdd...66cc4c3bbe4a

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[galaxyproject/galaxy] 20f98d: Finish job for Torque SSH runner
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20f98df554f502bddff1f22879bf867f97ab7288 https://github.com/galaxyproject/galaxy/commit/20f98df554f502bddff1f22879bf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Finish job for Torque SSH runner Commit: 61d25720661cb120afc7b44c57f41a1b245e21e4 https://github.com/galaxyproject/galaxy/commit/61d25720661cb120afc7b44c57f4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- More explcit logging of CLI runner state change (thx @nsoranzo) Commit: a3ac57dbc532320c98e0b4a72772663293ab3b06 https://github.com/galaxyproject/galaxy/commit/a3ac57dbc532320c98e0b4a72772… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove verbose_install_check option This option was introduced with #2554 and #2538, in reponse to a false positive conda install. This would have been caught by simply checking the exit code, which we are doing by default now. The additional verification is too strigent and not in line with the conda resolver. Activating this option will report perfectly well installed conda environments as having failed and will cause them to be uninstalled. Commit: d144f18e7a6eaa5276b2d63f51457eda1befd679 https://github.com/galaxyproject/galaxy/commit/d144f18e7a6eaa5276b2d63f5145… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fix typo in GIE nginx proxy docs Commit: b748ad1565a1e5064f6e08640c19b09a41b4b2bc https://github.com/galaxyproject/galaxy/commit/b748ad1565a1e5064f6e08640c19… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #3157 from galaxyproject/gie-doc-fix [16.07] Fix typo in GIE nginx proxy docs Commit: ae3bdf31dc815dfce305316fe67776bc6802ec1a https://github.com/galaxyproject/galaxy/commit/ae3bdf31dc815dfce305316fe677… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3127 from mvdbeek/remove_verbose_install_check_16.07 [16.07] Remove verbose_install_check option Commit: 727270261750fc71979e7ba9fec96b10091ff104 https://github.com/galaxyproject/galaxy/commit/727270261750fc71979e7ba9fec9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Merge pull request #3085 from mvdbeek/fix_torque_ssh [16.07] Finish job for Torque SSH/CLI runner Commit: ca4e8914ecddbba007c1f65ff17f51e719c0c149 https://github.com/galaxyproject/galaxy/commit/ca4e8914ecddbba007c1f65ff17f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M lib/galaxy/jobs/runners/cli.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/tools/deps/conda_util.py Compare: https://github.com/galaxyproject/galaxy/compare/bfabe00ea8f0...ca4e8914ecdd

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[galaxyproject/galaxy] 20f98d: Finish job for Torque SSH runner
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 20f98df554f502bddff1f22879bf867f97ab7288 https://github.com/galaxyproject/galaxy/commit/20f98df554f502bddff1f22879bf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Finish job for Torque SSH runner Commit: 61d25720661cb120afc7b44c57f41a1b245e21e4 https://github.com/galaxyproject/galaxy/commit/61d25720661cb120afc7b44c57f4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- More explcit logging of CLI runner state change (thx @nsoranzo) Commit: 727270261750fc71979e7ba9fec96b10091ff104 https://github.com/galaxyproject/galaxy/commit/727270261750fc71979e7ba9fec9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-14 (Mon, 14 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Merge pull request #3085 from mvdbeek/fix_torque_ssh [16.07] Finish job for Torque SSH/CLI runner Compare: https://github.com/galaxyproject/galaxy/compare/ae3bdf31dc81...727270261750

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[galaxyproject/galaxy] a3ac57: Remove verbose_install_check option
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: a3ac57dbc532320c98e0b4a72772663293ab3b06 https://github.com/galaxyproject/galaxy/commit/a3ac57dbc532320c98e0b4a72772… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove verbose_install_check option This option was introduced with #2554 and #2538, in reponse to a false positive conda install. This would have been caught by simply checking the exit code, which we are doing by default now. The additional verification is too strigent and not in line with the conda resolver. Activating this option will report perfectly well installed conda environments as having failed and will cause them to be uninstalled. Commit: ae3bdf31dc815dfce305316fe67776bc6802ec1a https://github.com/galaxyproject/galaxy/commit/ae3bdf31dc815dfce305316fe677… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3127 from mvdbeek/remove_verbose_install_check_16.07 [16.07] Remove verbose_install_check option Compare: https://github.com/galaxyproject/galaxy/compare/b748ad1565a1...ae3bdf31dc81

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[galaxyproject/galaxy] 510506: Rework dependency shell command handling
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51050653b44c24328d9225b69d9b1b6971b0354c https://github.com/galaxyproject/galaxy/commit/51050653b44c24328d9225b69d9b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-06 (Sun, 06 Nov 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Rework dependency shell command handling The approach is to always log a warning with stdout and stderr when the exit code is not 0. With this change, one can expect logs like the follwing: ``` galaxy.tools.deps.conda_util DEBUG 2016-11-05 15:14:17,373 Executing command: /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie(a)0.12.7 bowtie=0.12.7 127.0.0.1 - - [05/nov./2016:15:14:19 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36" 127.0.0.1 - - [05/nov./2016:15:14:22 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36" galaxy.tools.deps.conda_util WARNING 2016-11-05 15:14:24,029 Failed to execute command-line /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie(a)0.12.7 bowtie=0.12.7, stderr was: -------->>begin stderr<<-------- PackageNotFoundError: Package not found: '' Package missing in current linux-64 channels: - bowtie 0.12.7* You can search for packages on anaconda.org with anaconda search -t conda bowtie You may need to install the anaconda-client command line client with conda install anaconda-client -------->>end stderr<<-------- -------->>begin stdout<<-------- Fetching package metadata ............... Solving package specifications: . -------->>end stdout<<-------- galaxy.tools.deps.resolvers.conda DEBUG 2016-11-05 15:14:24,030 Removing failed conda install of bowtie, version '0.12.7' ``` This should be helpful for the more obscure errors that can occur with conda. Commit: bfabe00ea8f07782f0af307b124da8090f2906f2 https://github.com/galaxyproject/galaxy/commit/bfabe00ea8f07782f0af307b124d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3129 from mvdbeek/conda_error_reporting Pass dependency shell command errors to log Compare: https://github.com/galaxyproject/galaxy/compare/7955077e635f...bfabe00ea8f0

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[galaxyproject/galaxy] d3f751: Remove unnecessary set_output_history parameter
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3f7510b2db932228c76402062bad9095549f5f0 https://github.com/galaxyproject/galaxy/commit/d3f7510b2db932228c76402062ba… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Remove unnecessary set_output_history parameter Also fix import order and Python3 compatibility. Commit: 7955077e635f09b4a0c3fda621406686affe0c0f https://github.com/galaxyproject/galaxy/commit/7955077e635f09b4a0c3fda62140… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #3155 from nsoranzo/remove_set_output_history Remove unnecessary set_output_history parameter Compare: https://github.com/galaxyproject/galaxy/compare/46bd40bdc4c0...7955077e635f

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[galaxyproject/galaxy] 133fd3: Quote all paths in converter tools
by GitHub 14 Nov '16

14 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 133fd3adfc76216d8808ed7200e7278bdaf87488 https://github.com/galaxyproject/galaxy/commit/133fd3adfc76216d8808ed7200e7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml Log Message: ----------- Quote all paths in converter tools Commit: 89e6f77feb4404ecb9e0ba025b5d2168e627ed71 https://github.com/galaxyproject/galaxy/commit/89e6f77feb4404ecb9e0ba025b5d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml Log Message: ----------- Don't quote Commit: 46bd40bdc4c0dbad20084937e1e3ac606def9a3a https://github.com/galaxyproject/galaxy/commit/46bd40bdc4c0dbad20084937e1e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-13 (Sun, 13 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml Log Message: ----------- Merge pull request #3165 from mvdbeek/quote_data_converters Quote all paths in converter tool xml Compare: https://github.com/galaxyproject/galaxy/compare/3ec7be27952b...46bd40bdc4c0

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[galaxyproject/galaxy]
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/gie-doc-fix Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 019f55: Copy hid attribute to converted datasets for hdas ...
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 019f554e4e8425635c4ba36d7d2500d3a3a7502c https://github.com/galaxyproject/galaxy/commit/019f554e4e8425635c4ba36d7d25… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Copy hid attribute to converted datasets for hdas only Commit: 3ec7be27952b57cf7e0ad87fdf067cacc5e66856 https://github.com/galaxyproject/galaxy/commit/3ec7be27952b57cf7e0ad87fdf06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #3149 from guerler/fix_hid Explicitly specify attributes which should be copied to converted datasets Compare: https://github.com/galaxyproject/galaxy/compare/2d8cf6b3376b...3ec7be27952b

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[galaxyproject/galaxy] d144f1: Fix typo in GIE nginx proxy docs
by GitHub 11 Nov '16

11 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: d144f18e7a6eaa5276b2d63f51457eda1befd679 https://github.com/galaxyproject/galaxy/commit/d144f18e7a6eaa5276b2d63f5145… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fix typo in GIE nginx proxy docs Commit: b748ad1565a1e5064f6e08640c19b09a41b4b2bc https://github.com/galaxyproject/galaxy/commit/b748ad1565a1e5064f6e08640c19… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #3157 from galaxyproject/gie-doc-fix [16.07] Fix typo in GIE nginx proxy docs Compare: https://github.com/galaxyproject/galaxy/compare/53a66c9d4678...b748ad1565a1

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