{"action":"created","issue":{"url":"https://api.github.com/repos/DerrickWood/kraken/issues/60","repository_url":"https://api.github.com/repos/DerrickWood/kraken","labels_url":"https://api.github.com/repos/DerrickWood/kraken/issues/60/labels{/name}","comments_url":"https://api.github.com/repos/DerrickWood/kraken/issues/60/comments","events_url":"https://api.github.com/repos/DerrickWood/kraken/issues/60/events","html_url":"https://github.com/DerrickWood/kraken/issues/60","id":215711243,"number":60,"title":"kraken can't find jellyfish running within an HPCCluster","user":{"login":"GeoMicroSoares","id":14272488,"avatar_url":"https://avatars3.githubusercontent.com/u/14272488?v=4","gravatar_id":"","url":"https://api.github.com/users/GeoMicroSoares","html_url":"https://github.com/GeoMicroSoares","followers_url":"https://api.github.com/users/GeoMicroSoares/followers","following_url":"https://api.github.com/users/GeoMicroSoares/following{/other_user}","gists_url":"https://api.github.com/users/GeoMicroSoares/gists{/gist_id}","starred_url":"https://api.github.com/users/GeoMicroSoares/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GeoMicroSoares/subscriptions","organizations_url":"https://api.github.com/users/GeoMicroSoares/orgs","repos_url":"https://api.github.com/users/GeoMicroSoares/repos","events_url":"https://api.github.com/users/GeoMicroSoares/events{/privacy}","received_events_url":"https://api.github.com/users/GeoMicroSoares/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2017-03-21T11:47:43Z","updated_at":"2018-03-19T22:25:11Z","closed_at":"2017-06-06T08:31:14Z","author_association":"NONE","body":"kraken and jellyfish are installed to /kraken_install and /jellyfish-1.1.11 and all directories containing relevant executables have been added successfully to .bashrc\r\n \r\n```\r\n[ans74@hpc~]$ kraken-build\r\nMust select a task option.\r\nUsage: kraken-build [task option] [options]\r\n \r\nTask options (exactly one must be selected):\r\n--download-taxonomy        Download NCBI taxonomic information\r\n\r\n``` \r\n```\r\n[ans74@hpc~]$ jellyfish\r\nToo few arguments\r\nUsage: jellyfish <cmd> [options] arg...\r\nWhere <cmd> is one of: count, stats, histo, dump, merge, query, cite, qhisto, qdump, qmerge, jf.\r\nOptions:\r\n--version        Display version\r\n```\r\nrunning my script results in:\r\n```\r\n[ans74@hpc ~]$ cat kraken_3*\r\n/hpc/ans74/kraken_install/check_for_jellyfish.sh: line 27: jellyfish: command not found\r\n```\r\nhowever, running (not submitting) check_for_jellyfish.sh works!\r\n```\r\n[ans74@hpc ~]$ ./kraken_install/check_for_jellyfish.sh\r\nFound jellyfish v1.1.11\r\n```\r\nAlso, running the command I am trying to submitting to the HPC manually works:\r\n```\r\n[ans74@hpc ~]$ kraken-build --standard --db /hpc/scratch/ans74/kraken_database/\r\nFound jellyfish v1.1.11\r\n--2017-03-20 15:04:16--  ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz\r\n            => “gi_taxid_nucl.dmp.gz”\r\nResolving ftp.ncbi.nih.gov... 130.14.250.12, 2607:f220:41e:250::13\r\nConnecting to ftp.ncbi.nih.gov|130.14.250.12|:21... connected.\r\nLogging in as anonymous ... ^C\r\n```\r\nIs this somehow related to how kraken is written?\r\nDoes it make any sense that the executables are mapped into the .bashrc and work from there but then the script when submitted isn't able to detect jellyfish from the same directory?"},"comment":{"url":"https://api.github.com/repos/DerrickWood/kraken/issues/comments/374404095","html_url":"https://github.com/DerrickWood/kraken/issues/60#issuecomment-374404095","issue_url":"https://api.github.com/repos/DerrickWood/kraken/issues/60","id":374404095,"user":{"login":"katewd","id":19524262,"avatar_url":"https://avatars2.githubusercontent.com/u/19524262?v=4","gravatar_id":"","url":"https://api.github.com/users/katewd","html_url":"https://github.com/katewd","followers_url":"https://api.github.com/users/katewd/followers","following_url":"https://api.github.com/users/katewd/following{/other_user}","gists_url":"https://api.github.com/users/katewd/gists{/gist_id}","starred_url":"https://api.github.com/users/katewd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/katewd/subscriptions","organizations_url":"https://api.github.com/users/katewd/orgs","repos_url":"https://api.github.com/users/katewd/repos","events_url":"https://api.github.com/users/katewd/events{/privacy}","received_events_url":"https://api.github.com/users/katewd/received_events","type":"User","site_admin":false},"created_at":"2018-03-19T22:25:11Z","updated_at":"2018-03-19T22:25:11Z","author_association":"NONE","body":"For those who have the same problem I did when using Kraken and Jellyfish: \r\nI installed jellyfish v1.1.11 using sudo but then couldn't access the library created/needed when running kraken and jellyfish as 'me'. To get around this, I added the following line to my .bashrc file\r\n**export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/**\r\nAnd then it worked fine."}}
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