{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1625","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1625/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1625/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1625/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1625","id":187128206,"number":1625,"title":"bcbio_prepare_samples.py from docker","user":{"login":"silvanopiazza","id":1300855,"avatar_url":"https://avatars.githubusercontent.com/u/1300855?v=3","gravatar_id":"","url":"https://api.github.com/users/silvanopiazza","html_url":"https://github.com/silvanopiazza","followers_url":"https://api.github.com/users/silvanopiazza/followers","following_url":"https://api.github.com/users/silvanopiazza/following{/other_user}","gists_url":"https://api.github.com/users/silvanopiazza/gists{/gist_id}","starred_url":"https://api.github.com/users/silvanopiazza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/silvanopiazza/subscriptions","organizations_url":"https://api.github.com/users/silvanopiazza/orgs","repos_url":"https://api.github.com/users/silvanopiazza/repos","events_url":"https://api.github.com/users/silvanopiazza/events{/privacy}","received_events_url":"https://api.github.com/users/silvanopiazza/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-11-03T16:54:21Z","updated_at":"2016-11-05T09:54:33Z","closed_at":"2016-11-05T09:53:04Z","body":"Problem: can not use bcbio_prepare_samples.py from docker\r\n\r\nHi to all. \r\nI use BCBIO from docker official container.\r\nI notice that in the guide there was not suggesttion to create the soft link to bcbio_prepare_samples.py, so I did. \r\n_ln -s ~/install/bcbio-vm/anaconda/bin/bcbio_prepare_samples.py /usr/local/bin/ bcbio_prepare_samples.py\r\n\r\nBut if I call the script It was not able to find the config file., so I create a copy of it.\r\n\r\n_docker run bcbio/bcbio cat  /usr/local/share/bcbio-nextgen/config/bcbio_system.yaml > /media/silvano/Disk1/install/bcbio-vm/galaxy/bcbio_system.yaml_\r\n\r\nthen again if I try to launch the script I encounter a parse error, even if I use the csv structure from the guide.\r\n\r\n_$bcbio_prepare_samples.py --out merged --csv batch1.csv\r\nTraceback (most recent call last):\r\n  File \"/usr/local/bin/bcbio_prepare_samples.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==1.0.0a0', 'bcbio_prepare_samples.py')\r\n  File \"/local-storage/install/bcbio-vm/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 726, in run_script\r\n    \r\n  File \"/local-storage/install/bcbio-vm/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 1484, in run_script\r\n    \r\n  File \"/media/silvano/Disk1/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio_nextgen-1.0.0a0-py2.7.egg-info/scripts/bcbio_prepare_samples.py\", line 131, in <module>\r\n    samples = _get_samples_to_process(args.csv, out_dir, config)\r\n  File \"/media/silvano/Disk1/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio_nextgen-1.0.0a0-py2.7.egg-info/scripts/bcbio_prepare_samples.py\", line 48, in _get_samples_to_process\r\n    raise ValueError(\"Line needs 2 values: file and name.\")\r\n**ValueError: Line needs 2 values: file and name._**\r\n\r\nand\r\ncat batch1.csv\r\n/media/silvano/Disk1/data/batch_001/data/1PR20-M_S26_L001_R2_001.fastq.gz,ERR256785,batch1,normal,male,/media/silvano/Disk1/install/bcbio-vm/data/bed/MODY_6_FINAL_1_Regions_Export_cleanfile.bed\r\n/media/silvano/Disk1/data/batch_001/data/1PR20-M_S26_L001_R1_001.fastq.gz,ERR256786,batch1,normal,male,/media/silvano/Disk1/install/bcbio-vm/data/bed/MODY_6_FINAL_1_Regions_Export_cleanfile.bed\r\n\r\nany ideas?\r\n\r\nthank for any help\r\nSilvano\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/258601790","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1625#issuecomment-258601790","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1625","id":258601790,"user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=3","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"created_at":"2016-11-05T09:54:33Z","updated_at":"2016-11-05T09:54:33Z","body":"Silvano;\r\nSorry about the issue. This looks like the script might be complaining about an empty line in your input CSV file. The snippet you posted looks fine so I'd guess there are also some blank lines in there causing it to complain. If you remove those it should hopefully work correctly. I also pushed a fix to check for empty lines and fix this in the future. Hopefully it resolves the problem for you and gets things running cleanly."}}
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