{"action":"created","issue":{"url":"https://api.github.com/repos/LUMC/prinia/issues/1","repository_url":"https://api.github.com/repos/LUMC/prinia","labels_url":"https://api.github.com/repos/LUMC/prinia/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/LUMC/prinia/issues/1/comments","events_url":"https://api.github.com/repos/LUMC/prinia/issues/1/events","html_url":"https://github.com/LUMC/prinia/issues/1","id":364343041,"node_id":"MDU6SXNzdWUzNjQzNDMwNDE=","number":1,"title":"Primer3 crashes with exit code 255 when installed via conda","user":{"login":"sndrtj","id":7782240,"node_id":"MDQ6VXNlcjc3ODIyNDA=","avatar_url":"https://avatars3.githubusercontent.com/u/7782240?v=4","gravatar_id":"","url":"https://api.github.com/users/sndrtj","html_url":"https://github.com/sndrtj","followers_url":"https://api.github.com/users/sndrtj/followers","following_url":"https://api.github.com/users/sndrtj/following{/other_user}","gists_url":"https://api.github.com/users/sndrtj/gists{/gist_id}","starred_url":"https://api.github.com/users/sndrtj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sndrtj/subscriptions","organizations_url":"https://api.github.com/users/sndrtj/orgs","repos_url":"https://api.github.com/users/sndrtj/repos","events_url":"https://api.github.com/users/sndrtj/events{/privacy}","received_events_url":"https://api.github.com/users/sndrtj/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"sndrtj","id":7782240,"node_id":"MDQ6VXNlcjc3ODIyNDA=","avatar_url":"https://avatars3.githubusercontent.com/u/7782240?v=4","gravatar_id":"","url":"https://api.github.com/users/sndrtj","html_url":"https://github.com/sndrtj","followers_url":"https://api.github.com/users/sndrtj/followers","following_url":"https://api.github.com/users/sndrtj/following{/other_user}","gists_url":"https://api.github.com/users/sndrtj/gists{/gist_id}","starred_url":"https://api.github.com/users/sndrtj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sndrtj/subscriptions","organizations_url":"https://api.github.com/users/sndrtj/orgs","repos_url":"https://api.github.com/users/sndrtj/repos","events_url":"https://api.github.com/users/sndrtj/events{/privacy}","received_events_url":"https://api.github.com/users/sndrtj/received_events","type":"User","site_admin":false},"assignees":[{"login":"sndrtj","id":7782240,"node_id":"MDQ6VXNlcjc3ODIyNDA=","avatar_url":"https://avatars3.githubusercontent.com/u/7782240?v=4","gravatar_id":"","url":"https://api.github.com/users/sndrtj","html_url":"https://github.com/sndrtj","followers_url":"https://api.github.com/users/sndrtj/followers","following_url":"https://api.github.com/users/sndrtj/following{/other_user}","gists_url":"https://api.github.com/users/sndrtj/gists{/gist_id}","starred_url":"https://api.github.com/users/sndrtj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sndrtj/subscriptions","organizations_url":"https://api.github.com/users/sndrtj/orgs","repos_url":"https://api.github.com/users/sndrtj/repos","events_url":"https://api.github.com/users/sndrtj/events{/privacy}","received_events_url":"https://api.github.com/users/sndrtj/received_events","type":"User","site_admin":false}],"milestone":null,"comments":5,"created_at":"2018-09-27T07:39:35Z","updated_at":"2018-10-26T14:54:08Z","closed_at":"2018-10-11T12:09:45Z","author_association":"COLLABORATOR","body":"When installed via conda, the primer3 call ends with exit code 255. \r\nThe output file will contain the following message \r\n\r\n> Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified\r\n\r\nThis is due to conda installing the thermodynamic parameter configuration files in a non-standard location. The primer3 executable will look in two locations:\r\n\r\n1. `/opt/primer3_config`\r\n2. `./primer3_config`  \r\n\r\nConda installs those files in `$CONDA_ENV/share/primer3/primer3_config`. \r\n\r\nDebian-based systems on apt will actually install the files in `/etc/primer3_config`, but Debian has [pacthed](http://changelogs.ubuntu.com/changelogs/pool/universe/p/primer3/primer3_2.3.6-1/changelog) primer3 to look there as well. \r\n\r\nWe can set an extra parameter `PRIMER_THERMODYNAMIC_PARAMETERS_PATH ` to force primer3 to find its thermodynamic parameter configuration files."},"comment":{"url":"https://api.github.com/repos/LUMC/prinia/issues/comments/433435680","html_url":"https://github.com/LUMC/prinia/issues/1#issuecomment-433435680","issue_url":"https://api.github.com/repos/LUMC/prinia/issues/1","id":433435680,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMzQzNTY4MA==","user":{"login":"flacuchenta","id":43122347,"node_id":"MDQ6VXNlcjQzMTIyMzQ3","avatar_url":"https://avatars0.githubusercontent.com/u/43122347?v=4","gravatar_id":"","url":"https://api.github.com/users/flacuchenta","html_url":"https://github.com/flacuchenta","followers_url":"https://api.github.com/users/flacuchenta/followers","following_url":"https://api.github.com/users/flacuchenta/following{/other_user}","gists_url":"https://api.github.com/users/flacuchenta/gists{/gist_id}","starred_url":"https://api.github.com/users/flacuchenta/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/flacuchenta/subscriptions","organizations_url":"https://api.github.com/users/flacuchenta/orgs","repos_url":"https://api.github.com/users/flacuchenta/repos","events_url":"https://api.github.com/users/flacuchenta/events{/privacy}","received_events_url":"https://api.github.com/users/flacuchenta/received_events","type":"User","site_admin":false},"created_at":"2018-10-26T14:54:08Z","updated_at":"2018-10-26T14:54:08Z","author_association":"NONE","body":"Yes of course.\r\nis: primer3_core <unigenes.fasta.p3in> unigenes.fasta.p3out\r\nBut, only the first sequence is executed, then in the file unigenes.fasta.p3out, the error message appears as previously said. "}}
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