{"action":"created","issue":{"url":"https://api.github.com/repos/Oshlack/Clinker/issues/8","repository_url":"https://api.github.com/repos/Oshlack/Clinker","labels_url":"https://api.github.com/repos/Oshlack/Clinker/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/Oshlack/Clinker/issues/8/comments","events_url":"https://api.github.com/repos/Oshlack/Clinker/issues/8/events","html_url":"https://github.com/Oshlack/Clinker/issues/8","id":379138523,"node_id":"MDU6SXNzdWUzNzkxMzg1MjM=","number":8,"title":"Streamline installation process","user":{"login":"messersc","id":9218116,"node_id":"MDQ6VXNlcjkyMTgxMTY=","avatar_url":"https://avatars0.githubusercontent.com/u/9218116?v=4","gravatar_id":"","url":"https://api.github.com/users/messersc","html_url":"https://github.com/messersc","followers_url":"https://api.github.com/users/messersc/followers","following_url":"https://api.github.com/users/messersc/following{/other_user}","gists_url":"https://api.github.com/users/messersc/gists{/gist_id}","starred_url":"https://api.github.com/users/messersc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/messersc/subscriptions","organizations_url":"https://api.github.com/users/messersc/orgs","repos_url":"https://api.github.com/users/messersc/repos","events_url":"https://api.github.com/users/messersc/events{/privacy}","received_events_url":"https://api.github.com/users/messersc/received_events","type":"User","site_admin":false},"labels":[{"id":533842198,"node_id":"MDU6TGFiZWw1MzM4NDIxOTg=","url":"https://api.github.com/repos/Oshlack/Clinker/labels/enhancement","name":"enhancement","color":"84b6eb","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-11-09T12:12:01Z","updated_at":"2018-11-15T14:43:12Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nthe current installation is a little cumbersome and I think we can make it easier with little effort. The reason is that all the software that gets installed outside of conda right now if you follow the wiki page is also available through conda. In the end, of course it would be very nice if Clinker itself would also make to bioconda.\r\n\r\nShort-term, we can aim for an `environment.yaml` file (https://conda.io/docs/user-guide/tasks/manage-environments.html#create-env-file-manually).\r\n\r\nNote that the conda `r` channel is not needed anymore, if we use the multichannel `defaults` (https://github.com/conda/conda/issues/7695#issuecomment-416350450)\r\n\r\nFor example:\r\n\r\n```yaml\r\nname: clinker\r\nchannels:\r\n  - defaults\r\n  - bioconda\r\n  - conda-forge\r\ndependencies:\r\n  - python=2.7\r\n  - star=2.5.3a\r\n  - samtools\r\n  - bpipe\r\n  - bioconductor-gviz # pulls biomart, R\r\n  - libiconv\r\n```\r\n\r\nThe above is untested, I'll let you know how it goes and then we can decide what the best course of action is.\r\n\r\nClemens"},"comment":{"url":"https://api.github.com/repos/Oshlack/Clinker/issues/comments/439063319","html_url":"https://github.com/Oshlack/Clinker/issues/8#issuecomment-439063319","issue_url":"https://api.github.com/repos/Oshlack/Clinker/issues/8","id":439063319,"node_id":"MDEyOklzc3VlQ29tbWVudDQzOTA2MzMxOQ==","user":{"login":"messersc","id":9218116,"node_id":"MDQ6VXNlcjkyMTgxMTY=","avatar_url":"https://avatars0.githubusercontent.com/u/9218116?v=4","gravatar_id":"","url":"https://api.github.com/users/messersc","html_url":"https://github.com/messersc","followers_url":"https://api.github.com/users/messersc/followers","following_url":"https://api.github.com/users/messersc/following{/other_user}","gists_url":"https://api.github.com/users/messersc/gists{/gist_id}","starred_url":"https://api.github.com/users/messersc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/messersc/subscriptions","organizations_url":"https://api.github.com/users/messersc/orgs","repos_url":"https://api.github.com/users/messersc/repos","events_url":"https://api.github.com/users/messersc/events{/privacy}","received_events_url":"https://api.github.com/users/messersc/received_events","type":"User","site_admin":false},"created_at":"2018-11-15T14:43:12Z","updated_at":"2018-11-15T14:43:12Z","author_association":"NONE","body":"I see, I only checked the package search and not the recipes. But this is really strange, it was merged into master but apparently there is no package...\r\n\r\nI added `libiconv` above, which was missing and I also had some problems with `bioconductor-genomeinfodb` and `bioconductor-genomeinfodbdata`, where apparently the conda packages did not work and I needed to install from bioconductor directly.\r\n\r\nBut first, we really need to find out why this package does not show up..."}}
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