{"push_id":1402054767,"size":19,"distinct_size":19,"ref":"refs/heads/dev","head":"66cc4c3bbe4a90cd68d935574691c31b8053804e","before":"2d8cf6b3376b41a6dd9a9ff3f4a82aaae1baa209","commits":[{"sha":"20f98df554f502bddff1f22879bf867f97ab7288","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Finish job for Torque SSH runner","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/20f98df554f502bddff1f22879bf867f97ab7288"},{"sha":"61d25720661cb120afc7b44c57f41a1b245e21e4","author":{"name":"Marius van den Beek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"More explcit logging of CLI runner state change (thx @nsoranzo)","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/61d25720661cb120afc7b44c57f41a1b245e21e4"},{"sha":"a3ac57dbc532320c98e0b4a72772663293ab3b06","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Remove verbose_install_check option\n\nThis option was introduced with #2554 and #2538, in reponse to a false\npositive conda install.  This would have been caught by simply checking\nthe exit code, which we are doing by default now. The additional\nverification is too strigent and not in line with the conda resolver.\nActivating this option will report perfectly well installed conda\nenvironments as having failed and will cause them to be uninstalled.","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/a3ac57dbc532320c98e0b4a72772663293ab3b06"},{"sha":"51050653b44c24328d9225b69d9b1b6971b0354c","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Rework dependency shell command handling\n\nThe approach is to always log a warning with stdout and stderr when\nthe exit code is not 0.\nWith this change, one can expect logs like the follwing:\n```\ngalaxy.tools.deps.conda_util DEBUG 2016-11-05 15:14:17,373 Executing command: /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie@0.12.7 bowtie=0.12.7\n127.0.0.1 - - [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\"\n127.0.0.1 - - [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\"\ngalaxy.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@0.12.7 bowtie=0.12.7, stderr was:\n-------->>begin stderr<<--------\n\nPackageNotFoundError: Package not found: '' Package missing in current linux-64 channels:\n  - bowtie 0.12.7*\n\nYou can search for packages on anaconda.org with\n\n    anaconda search -t conda bowtie\n\nYou may need to install the anaconda-client command line client with\n\n    conda install anaconda-client\n\n-------->>end stderr<<--------\n-------->>begin stdout<<--------\nFetching package metadata ...............\nSolving package specifications: .\n\n-------->>end stdout<<--------\n\ngalaxy.tools.deps.resolvers.conda DEBUG 2016-11-05 15:14:24,030 Removing failed conda install of bowtie, version '0.12.7'\n```\nThis should be helpful for the more obscure errors that can occur with conda.","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/51050653b44c24328d9225b69d9b1b6971b0354c"},{"sha":"019f554e4e8425635c4ba36d7d2500d3a3a7502c","author":{"name":"guerler","email":"e835d2f577b256a396d1625aff388872787f9585@gmail.com"},"message":"Copy hid attribute to converted datasets for hdas only","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/019f554e4e8425635c4ba36d7d2500d3a3a7502c"},{"sha":"d144f18e7a6eaa5276b2d63f51457eda1befd679","author":{"name":"Nate 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datasets","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/3ec7be27952b57cf7e0ad87fdf067cacc5e66856"},{"sha":"d3f7510b2db932228c76402062bad9095549f5f0","author":{"name":"Nicola Soranzo","email":"0a32b153982c365f1166dea2b0e00380b88c503a@tgac.ac.uk"},"message":"Remove unnecessary set_output_history parameter\n\nAlso fix import order and Python3 compatibility.","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/d3f7510b2db932228c76402062bad9095549f5f0"},{"sha":"133fd3adfc76216d8808ed7200e7278bdaf87488","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Quote all paths in converter tools","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/133fd3adfc76216d8808ed7200e7278bdaf87488"},{"sha":"89e6f77feb4404ecb9e0ba025b5d2168e627ed71","author":{"name":"mvdbeek","email":"956c6368fd22c4d37e64fb8545c7be9ca0132de1@gmail.com"},"message":"Don't quote","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/89e6f77feb4404ecb9e0ba025b5d2168e627ed71"},{"sha":"46bd40bdc4c0dbad20084937e1e3ac606def9a3a","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Merge pull request #3165 from mvdbeek/quote_data_converters\n\nQuote all paths in converter tool xml","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/46bd40bdc4c0dbad20084937e1e3ac606def9a3a"},{"sha":"7955077e635f09b4a0c3fda621406686affe0c0f","author":{"name":"John Chilton","email":"006bba88ddf60ee719290411dd4f347fca0a9729@gmail.com"},"message":"Merge pull request #3155 from nsoranzo/remove_set_output_history\n\nRemove unnecessary set_output_history parameter","distinct":true,"url":"https://api.github.com/repos/gregvonkuster/galaxy/commits/7955077e635f09b4a0c3fda621406686affe0c0f"},{"sha":"bfabe00ea8f07782f0af307b124da8090f2906f2","author":{"name":"John 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