{"action":"created","issue":{"url":"https://api.github.com/repos/rcgsheffield/iceberg_software/issues/272","repository_url":"https://api.github.com/repos/rcgsheffield/iceberg_software","labels_url":"https://api.github.com/repos/rcgsheffield/iceberg_software/issues/272/labels{/name}","comments_url":"https://api.github.com/repos/rcgsheffield/iceberg_software/issues/272/comments","events_url":"https://api.github.com/repos/rcgsheffield/iceberg_software/issues/272/events","html_url":"https://github.com/rcgsheffield/iceberg_software/issues/272","id":137265513,"number":272,"title":"bcbio -- mm10 not found error","user":{"login":"ssamberkar","id":9107374,"avatar_url":"https://avatars.githubusercontent.com/u/9107374?v=3","gravatar_id":"","url":"https://api.github.com/users/ssamberkar","html_url":"https://github.com/ssamberkar","followers_url":"https://api.github.com/users/ssamberkar/followers","following_url":"https://api.github.com/users/ssamberkar/following{/other_user}","gists_url":"https://api.github.com/users/ssamberkar/gists{/gist_id}","starred_url":"https://api.github.com/users/ssamberkar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ssamberkar/subscriptions","organizations_url":"https://api.github.com/users/ssamberkar/orgs","repos_url":"https://api.github.com/users/ssamberkar/repos","events_url":"https://api.github.com/users/ssamberkar/events{/privacy}","received_events_url":"https://api.github.com/users/ssamberkar/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-02-29T14:11:28Z","updated_at":"2016-02-29T16:26:11Z","closed_at":null,"body":"Hi Mike (@roryk) and Mike (@mikecroucher),\r\n\r\nAlthough mm10 has been installed with all index files required for star, looks like some intermediary files are missing. This is the error I'm getting at when I try running my mouse samples with mm10.\r\n\r\n```\r\nTraceback (most recent call last):\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a//tools/bin/bcbio_nextgen.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.6', 'bcbio_nextgen.py')\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/setuptools-19.6.2-py2.7.egg/pkg_resources/__init__.py\", line 724, in run_script\r\n    \r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/setuptools-19.6.2-py2.7.egg/pkg_resources/__init__.py\", line 1649, in run_script\r\n    \r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.6-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.6-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 39, in run_main\r\n    fc_dir, run_info_yaml)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 82, in _run_toplevel\r\n    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 233, in rnaseqpipeline\r\n    samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 357, in rnaseq_prep_samples\r\n    [x[0][\"description\"] for x in samples]]])\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 28, in run_parallel\r\n    return run_multicore(fn, items, config, parallel=parallel)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 86, in run_multicore\r\n    for data in joblib.Parallel(parallel[\"num_jobs\"])(joblib.delayed(fn)(x) for x in items):\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 804, in __call__\r\n    while self.dispatch_one_batch(iterator):\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 662, in dispatch_one_batch\r\n    self._dispatch(tasks)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 570, in _dispatch\r\n    job = ImmediateComputeBatch(batch)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 183, in __init__\r\n    self.results = batch()\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 72, in __call__\r\n    return [func(*args, **kwargs) for func, args, kwargs in self.items]\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 50, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 255, in organize_samples\r\n    return run_info.organize(*args)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 58, in organize\r\n    item = add_reference_resources(item)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 145, in add_reference_resources\r\n    data[\"reference\"] = genome.get_refs(data[\"genome_build\"], aligner, data[\"dirs\"][\"galaxy\"], data)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/genome.py\", line 199, in get_refs\r\n    galaxy_config, data)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/genome.py\", line 151, in _get_ref_from_galaxy_loc\r\n    cur_ref = download_prepped_genome(genome_build, data, name, need_remap)\r\n  File \"/usr/local/packages6/apps/gcc/5.2/bcbio/0.9.6a/anaconda/lib/python2.7/site-packages/bcbio/pipeline/genome.py\", line 261, in download_prepped_genome\r\n    raise ValueError(\"Could not find reference genome file %s %s\" % (genome_build, name))\r\nValueError: Could not find reference genome file mm10 samtools\r\n\r\n```"},"comment":{"url":"https://api.github.com/repos/rcgsheffield/iceberg_software/issues/comments/190276622","html_url":"https://github.com/rcgsheffield/iceberg_software/issues/272#issuecomment-190276622","issue_url":"https://api.github.com/repos/rcgsheffield/iceberg_software/issues/272","id":190276622,"user":{"login":"roryk","id":414586,"avatar_url":"https://avatars.githubusercontent.com/u/414586?v=3","gravatar_id":"","url":"https://api.github.com/users/roryk","html_url":"https://github.com/roryk","followers_url":"https://api.github.com/users/roryk/followers","following_url":"https://api.github.com/users/roryk/following{/other_user}","gists_url":"https://api.github.com/users/roryk/gists{/gist_id}","starred_url":"https://api.github.com/users/roryk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roryk/subscriptions","organizations_url":"https://api.github.com/users/roryk/orgs","repos_url":"https://api.github.com/users/roryk/repos","events_url":"https://api.github.com/users/roryk/events{/privacy}","received_events_url":"https://api.github.com/users/roryk/received_events","type":"User","site_admin":false},"created_at":"2016-02-29T16:26:11Z","updated_at":"2016-02-29T16:26:11Z","body":"Hi Sandeep,\n\nIt will work if you add it manually, but it should have been put in there in the first place. For new genomes, bcbio_setup_genome.py will update that file and put the entry there. I’m not sure why installing with bcbio_nextgen.py upgrade did not add it.\n\nBest,\n\nRory\n\n> On Feb 29, 2016, at 11:06 AM, Sandeep Amberkar <notifications@github.com> wrote:\n> \n> You're right, it is missing the mm10 entry.\n> Will it work if I add it manually?\n> How to fix it during installation itself, say for adding another genome for another organism, if the same issue arises?\n> \n> —\n> Reply to this email directly or view it on GitHub <https://github.com/rcgsheffield/iceberg_software/issues/272#issuecomment-190270329>.\n> \n\n"}}