{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1410","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1410/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1410/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1410/events","html_url":"https://github.com/galaxyproject/galaxy/pull/1410","id":124470762,"number":1410,"title":"all commands in new isolated shell","user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/status/WIP","name":"status/WIP","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":11,"created_at":"2015-12-31T13:25:10Z","updated_at":"2016-01-03T00:36:25Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1410","html_url":"https://github.com/galaxyproject/galaxy/pull/1410","diff_url":"https://github.com/galaxyproject/galaxy/pull/1410.diff","patch_url":"https://github.com/galaxyproject/galaxy/pull/1410.patch"},"body":"Remove `enable_beta_tool_command_isolation` from galaxy.ini and activate it by default.\r\n\r\nThis is more and more essential for tools that are depending on their own python version."},"comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments/168445533","html_url":"https://github.com/galaxyproject/galaxy/pull/1410#issuecomment-168445533","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1410","id":168445533,"user":{"login":"gregvonkuster","id":6947053,"avatar_url":"https://avatars.githubusercontent.com/u/6947053?v=3","gravatar_id":"","url":"https://api.github.com/users/gregvonkuster","html_url":"https://github.com/gregvonkuster","followers_url":"https://api.github.com/users/gregvonkuster/followers","following_url":"https://api.github.com/users/gregvonkuster/following{/other_user}","gists_url":"https://api.github.com/users/gregvonkuster/gists{/gist_id}","starred_url":"https://api.github.com/users/gregvonkuster/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregvonkuster/subscriptions","organizations_url":"https://api.github.com/users/gregvonkuster/orgs","repos_url":"https://api.github.com/users/gregvonkuster/repos","events_url":"https://api.github.com/users/gregvonkuster/events{/privacy}","received_events_url":"https://api.github.com/users/gregvonkuster/received_events","type":"User","site_admin":false},"created_at":"2016-01-03T00:36:25Z","updated_at":"2016-01-03T00:36:25Z","body":"@jmchilton I cloned a new dev branch and applied your patch as follows (I had previously downloaded it into my_patch).  Let me know if there's a better way to do this.\r\nMacBook-Pro-2:galaxy gvk$ git apply --stat my_patch \r\n config/galaxy.ini.sample               |    7 ++++--\r\n lib/galaxy/config.py                   |    2 +-\r\n test/unit/jobs/test_command_factory.py |   28 +++++++++++++++++++++++---\r\n lib/galaxy/jobs/__init__.py            |   35 ++++++++++++++++++++------------\r\n lib/galaxy/jobs/command_factory.py     |    9 +++++---\r\n lib/galaxy/jobs/command_factory.py     |    4 ++--\r\n lib/galaxy/jobs/command_factory.py     |    5 +++--\r\n 7 files changed, 63 insertions(+), 27 deletions(-)\r\n\r\nI set the following in galaxy.ini:\r\nenable_beta_tool_command_isolation = True\r\n\r\nI then ran the same bwa job I had run several months ago that uncovered this problem at that time and see the same exception:\r\n\r\nTraceback (most recent call last):\r\n  File \"/Users/gvk/work/galaxy/lib/galaxy/jobs/runners/local.py\", line 128, in queue_job\r\n    job_wrapper.finish( stdout, stderr, exit_code )\r\n  File \"/Users/gvk/work/galaxy/lib/galaxy/jobs/__init__.py\", line 1206, in finish\r\n    dataset.datatype.set_meta( dataset, overwrite=False )\r\n  File \"/Users/gvk/work/galaxy/lib/galaxy/datatypes/binary.py\", line 309, in set_meta\r\n    exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )\r\n  File \"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py\", line 522, in call\r\n    return Popen(*popenargs, **kwargs).wait()\r\n  File \"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py\", line 710, in __init__\r\n    errread, errwrite)\r\n  File \"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py\", line 1327, in _execute_child\r\n    raise child_exception\r\nOSError: [Errno 2] No such file or directory\r\n"}}