{"action":"created","issue":{"url":"https://api.github.com/repos/databio/hub.bulker.io/issues/3","repository_url":"https://api.github.com/repos/databio/hub.bulker.io","labels_url":"https://api.github.com/repos/databio/hub.bulker.io/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/databio/hub.bulker.io/issues/3/comments","events_url":"https://api.github.com/repos/databio/hub.bulker.io/issues/3/events","html_url":"https://github.com/databio/hub.bulker.io/issues/3","id":507205426,"node_id":"MDU6SXNzdWU1MDcyMDU0MjY=","number":3,"title":"refgenie manifest bismark container doesn't contain bowtie2-build","user":{"login":"nsheff","id":5271009,"node_id":"MDQ6VXNlcjUyNzEwMDk=","avatar_url":"https://avatars2.githubusercontent.com/u/5271009?v=4","gravatar_id":"","url":"https://api.github.com/users/nsheff","html_url":"https://github.com/nsheff","followers_url":"https://api.github.com/users/nsheff/followers","following_url":"https://api.github.com/users/nsheff/following{/other_user}","gists_url":"https://api.github.com/users/nsheff/gists{/gist_id}","starred_url":"https://api.github.com/users/nsheff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nsheff/subscriptions","organizations_url":"https://api.github.com/users/nsheff/orgs","repos_url":"https://api.github.com/users/nsheff/repos","events_url":"https://api.github.com/users/nsheff/events{/privacy}","received_events_url":"https://api.github.com/users/nsheff/received_events","type":"User","site_admin":false},"labels":[{"id":1579787983,"node_id":"MDU6TGFiZWwxNTc5Nzg3OTgz","url":"https://api.github.com/repos/databio/hub.bulker.io/labels/bug","name":"bug","color":"d73a4a","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2019-10-15T12:15:57Z","updated_at":"2019-10-15T12:30:09Z","closed_at":null,"author_association":"MEMBER","body":"bismark_genome_preparation doesn't work for me because the container doesn't contain bowtie2-build -- did you test this @michalstolarczyk ?\r\n\r\n```\r\nbismark_genome_preparation --bowtie2 /home/nsheff/sandbox/refgenie_bulker/hs38d1/bismark_bt2_index/default\r\nWriting bisulfite genomes out into a single MFA (multi FastA) file\r\n\r\nBisulfite Genome Indexer version v0.17.0 (last modified 07 November 2016)\r\n\r\nA directory called /home/nsheff/sandbox/refgenie_bulker/hs38d1/bismark_bt2_index/default/Bisulfite_Genome/ already exists. Bisulfite converted sequences and/or already existing Bowtie (1 or 2) indices will be overwritten!\r\n\r\n\r\nStep I - Prepare genome folders - completed\r\n\r\n\r\n\r\nTotal number of conversions performed:\r\nC->T:   1274343\r\nG->A:   1235129\r\nPlease be aware that this process can - depending on genome size - take several hours!\r\n\r\nStep II - Genome bisulfite conversions - completed\r\n\r\n\r\nBismark Genome Preparation - Step III: Launching the Bowtie 2 indexer\r\nCan't exec \"bowtie2-build\": No such file or directory at /usr/local/bin/bismark_genome_preparation line 178, <IN> line 75966.\r\nParent process: Failed to build index\r\n```"},"comment":{"url":"https://api.github.com/repos/databio/hub.bulker.io/issues/comments/542187358","html_url":"https://github.com/databio/hub.bulker.io/issues/3#issuecomment-542187358","issue_url":"https://api.github.com/repos/databio/hub.bulker.io/issues/3","id":542187358,"node_id":"MDEyOklzc3VlQ29tbWVudDU0MjE4NzM1OA==","user":{"login":"michalstolarczyk","id":22797900,"node_id":"MDQ6VXNlcjIyNzk3OTAw","avatar_url":"https://avatars2.githubusercontent.com/u/22797900?v=4","gravatar_id":"","url":"https://api.github.com/users/michalstolarczyk","html_url":"https://github.com/michalstolarczyk","followers_url":"https://api.github.com/users/michalstolarczyk/followers","following_url":"https://api.github.com/users/michalstolarczyk/following{/other_user}","gists_url":"https://api.github.com/users/michalstolarczyk/gists{/gist_id}","starred_url":"https://api.github.com/users/michalstolarczyk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/michalstolarczyk/subscriptions","organizations_url":"https://api.github.com/users/michalstolarczyk/orgs","repos_url":"https://api.github.com/users/michalstolarczyk/repos","events_url":"https://api.github.com/users/michalstolarczyk/events{/privacy}","received_events_url":"https://api.github.com/users/michalstolarczyk/received_events","type":"User","site_admin":false},"created_at":"2019-10-15T12:30:09Z","updated_at":"2019-10-15T12:30:09Z","author_association":"MEMBER","body":"> So, I guess the only solution I can think of is to build a different container that also contains bowtie2 \r\n\r\nthis is what I wanted to do\r\n\r\nI'll also let them know about the issue with the container"}}
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