{"action":"created","issue":{"url":"https://api.github.com/repos/BioDocker/biodocker/issues/50","repository_url":"https://api.github.com/repos/BioDocker/biodocker","labels_url":"https://api.github.com/repos/BioDocker/biodocker/issues/50/labels{/name}","comments_url":"https://api.github.com/repos/BioDocker/biodocker/issues/50/comments","events_url":"https://api.github.com/repos/BioDocker/biodocker/issues/50/events","html_url":"https://github.com/BioDocker/biodocker/issues/50","id":156670224,"number":50,"title":"Some comments in the current guidelines","user":{"login":"ypriverol","id":52113,"avatar_url":"https://avatars.githubusercontent.com/u/52113?v=3","gravatar_id":"","url":"https://api.github.com/users/ypriverol","html_url":"https://github.com/ypriverol","followers_url":"https://api.github.com/users/ypriverol/followers","following_url":"https://api.github.com/users/ypriverol/following{/other_user}","gists_url":"https://api.github.com/users/ypriverol/gists{/gist_id}","starred_url":"https://api.github.com/users/ypriverol/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ypriverol/subscriptions","organizations_url":"https://api.github.com/users/ypriverol/orgs","repos_url":"https://api.github.com/users/ypriverol/repos","events_url":"https://api.github.com/users/ypriverol/events{/privacy}","received_events_url":"https://api.github.com/users/ypriverol/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/BioDocker/biodocker/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/BioDocker/biodocker/labels/help%20wanted","name":"help wanted","color":"159818"}],"state":"open","locked":false,"assignee":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"milestone":null,"comments":3,"created_at":"2016-05-25T06:06:02Z","updated_at":"2016-05-27T08:28:10Z","closed_at":null,"body":"This are some questions from a user:\r\n\r\n>In many of your docker files I see that you change to a biodocker user or that you set as working directory the directory of a tool, but I was wondering is those behaviours are indicated somewhere, are they necessary requirements, etc. As a sideline to this, in one of our important use cases — running galaxy with dockerized tools within a container orchestration environment — having the containerised tool running ability bound to be in a defined working directory breaks things. I’m not saying that you’re actively doing this, but if that is the reason for setting the working directory on the docker file, then it would be a problem for us. This is because galaxy needs to control working directories to detect variably named output files. The only case where we see this happening is when the main entrypoint is something like <interpreter> <scriptOnWorkingDirectory>, like Rscript myScript.R (receiving arguments from the outside). Our current solution to this is to wrap this call in shell file, pass arguments to the wrapped call, leave this wrapper in the path and make it executable.\r\n\r\n> Another question. We are currently building docker files within the our project for a number of metabolomics tools. However, for project reporting statistics and deliverables, we need to keep this under the ownership of the our github organization. Do you see a way in which we could both host these docker files in our github repo while also making them available at the biodocker repo? Would the git submodules work for this? "},"comment":{"url":"https://api.github.com/repos/BioDocker/biodocker/issues/comments/222090085","html_url":"https://github.com/BioDocker/biodocker/issues/50#issuecomment-222090085","issue_url":"https://api.github.com/repos/BioDocker/biodocker/issues/50","id":222090085,"user":{"login":"ypriverol","id":52113,"avatar_url":"https://avatars.githubusercontent.com/u/52113?v=3","gravatar_id":"","url":"https://api.github.com/users/ypriverol","html_url":"https://github.com/ypriverol","followers_url":"https://api.github.com/users/ypriverol/followers","following_url":"https://api.github.com/users/ypriverol/following{/other_user}","gists_url":"https://api.github.com/users/ypriverol/gists{/gist_id}","starred_url":"https://api.github.com/users/ypriverol/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ypriverol/subscriptions","organizations_url":"https://api.github.com/users/ypriverol/orgs","repos_url":"https://api.github.com/users/ypriverol/repos","events_url":"https://api.github.com/users/ypriverol/events{/privacy}","received_events_url":"https://api.github.com/users/ypriverol/received_events","type":"User","site_admin":false},"created_at":"2016-05-27T08:28:10Z","updated_at":"2016-05-27T08:28:10Z","body":"> @prvst Where is defined the first two points?. "}}
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