{"action":"created","issue":{"url":"https://api.github.com/repos/montilab/Hydra/issues/31","repository_url":"https://api.github.com/repos/montilab/Hydra","labels_url":"https://api.github.com/repos/montilab/Hydra/issues/31/labels{/name}","comments_url":"https://api.github.com/repos/montilab/Hydra/issues/31/comments","events_url":"https://api.github.com/repos/montilab/Hydra/issues/31/events","html_url":"https://github.com/montilab/Hydra/issues/31","id":188832546,"number":31,"title":"pipeline.py issues","user":{"login":"ericreed","id":6471317,"avatar_url":"https://avatars.githubusercontent.com/u/6471317?v=3","gravatar_id":"","url":"https://api.github.com/users/ericreed","html_url":"https://github.com/ericreed","followers_url":"https://api.github.com/users/ericreed/followers","following_url":"https://api.github.com/users/ericreed/following{/other_user}","gists_url":"https://api.github.com/users/ericreed/gists{/gist_id}","starred_url":"https://api.github.com/users/ericreed/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ericreed/subscriptions","organizations_url":"https://api.github.com/users/ericreed/orgs","repos_url":"https://api.github.com/users/ericreed/repos","events_url":"https://api.github.com/users/ericreed/events{/privacy}","received_events_url":"https://api.github.com/users/ericreed/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2016-11-11T19:29:33Z","updated_at":"2016-12-08T19:47:26Z","closed_at":null,"body":"I'm having trouble getting a bowtie2 module (bowtie2.py).\r\n\r\nAmong the other necessary changes to pipeline.py, I've added...\r\n\r\n            **elif param['aligner'] == 'bowtie2':\r\n                #running the aligner\r\n                HELPER.submit_job(param,\r\n                                  'run_bowtie2',\r\n                                  input_files='fastq_files',\r\n                                  output_files='bam_files',\r\n                                  cores=param['qsub_num_processors'],\r\n                                  mem_free='32G')**\r\n\r\nAfter running python setup.py install, I can see that run_bowtie2 has been added to the dev_env/bin directory.  However, when I try to run the updated version of Hydra, I get the error:\r\n\r\n**The selected aligner does not exist.**\r\n\r\nIn my parameter file I have set the aligner to:\r\n\r\n**aligner   =    bowtie2**\r\n\r\nAny thoughts to what could be preventing pipeline.py from updating?\r\n\r\nEric"},"comment":{"url":"https://api.github.com/repos/montilab/Hydra/issues/comments/265836228","html_url":"https://github.com/montilab/Hydra/issues/31#issuecomment-265836228","issue_url":"https://api.github.com/repos/montilab/Hydra/issues/31","id":265836228,"user":{"login":"ericreed","id":6471317,"avatar_url":"https://avatars.githubusercontent.com/u/6471317?v=3","gravatar_id":"","url":"https://api.github.com/users/ericreed","html_url":"https://github.com/ericreed","followers_url":"https://api.github.com/users/ericreed/followers","following_url":"https://api.github.com/users/ericreed/following{/other_user}","gists_url":"https://api.github.com/users/ericreed/gists{/gist_id}","starred_url":"https://api.github.com/users/ericreed/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ericreed/subscriptions","organizations_url":"https://api.github.com/users/ericreed/orgs","repos_url":"https://api.github.com/users/ericreed/repos","events_url":"https://api.github.com/users/ericreed/events{/privacy}","received_events_url":"https://api.github.com/users/ericreed/received_events","type":"User","site_admin":false},"created_at":"2016-12-08T19:47:26Z","updated_at":"2016-12-08T19:47:26Z","body":"I figured it out.  Deleting **dev_env/bin/hydra-rnaseq** prior to running **python setup.py install** fixes this."}}
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