{"action":"created","issue":{"url":"https://api.github.com/repos/nf-core/cookiecutter/issues/29","repository_url":"https://api.github.com/repos/nf-core/cookiecutter","labels_url":"https://api.github.com/repos/nf-core/cookiecutter/issues/29/labels{/name}","comments_url":"https://api.github.com/repos/nf-core/cookiecutter/issues/29/comments","events_url":"https://api.github.com/repos/nf-core/cookiecutter/issues/29/events","html_url":"https://github.com/nf-core/cookiecutter/issues/29","id":327051002,"number":29,"title":"Don't use bioconda environments in docker image","user":{"login":"ewels","id":465550,"avatar_url":"https://avatars3.githubusercontent.com/u/465550?v=4","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"labels":[{"id":784050542,"url":"https://api.github.com/repos/nf-core/cookiecutter/labels/enhancement","name":"enhancement","color":"84b6eb","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-05-28T14:50:01Z","updated_at":"2018-05-29T11:54:44Z","closed_at":null,"author_association":"MEMBER","body":"See https://github.com/nf-core/chipseq/pull/10#issue-190796115 by @tiagochst:\r\n\r\n---\r\n\r\n-  Changed `RUN conda env create -f /environment.yml `to `RUN conda env update -n root --file environment.yml ` because of the source below:\r\n    * > _If you are using the Conda package manager, avoid creating a Conda environment. Instead, update the root environment with whatever dependencies you want to install._\r\n      > \r\n      > _As an example to the above warning, it would be best practice to run this: `RUN conda env update -n root --file environment.yml` and avoid this: `RUN conda env create -f environment.yml`_\r\n\r\nhttps://docs.datascience.com/en/master/appendix-1/dockerfile-basics-and-best-practices-1.html\r\n\r\n---\r\n\r\nWe should update all pipelines to use this method."},"comment":{"url":"https://api.github.com/repos/nf-core/cookiecutter/issues/comments/392749722","html_url":"https://github.com/nf-core/cookiecutter/issues/29#issuecomment-392749722","issue_url":"https://api.github.com/repos/nf-core/cookiecutter/issues/29","id":392749722,"user":{"login":"tiagochst","id":145529,"avatar_url":"https://avatars0.githubusercontent.com/u/145529?v=4","gravatar_id":"","url":"https://api.github.com/users/tiagochst","html_url":"https://github.com/tiagochst","followers_url":"https://api.github.com/users/tiagochst/followers","following_url":"https://api.github.com/users/tiagochst/following{/other_user}","gists_url":"https://api.github.com/users/tiagochst/gists{/gist_id}","starred_url":"https://api.github.com/users/tiagochst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tiagochst/subscriptions","organizations_url":"https://api.github.com/users/tiagochst/orgs","repos_url":"https://api.github.com/users/tiagochst/repos","events_url":"https://api.github.com/users/tiagochst/events{/privacy}","received_events_url":"https://api.github.com/users/tiagochst/received_events","type":"User","site_admin":false},"created_at":"2018-05-29T11:54:44Z","updated_at":"2018-05-29T11:54:44Z","author_association":"NONE","body":"You can keep the old way if it was working and it was just a warning. I don't know the reason why use one instead of the another unless I ask who wrote the documentation.\r\n\r\nI'm not sure how I came to that documentation. But,  I would say I found that by chance (I was looking to use conda with github repo, If I'm not wrong) and decided to change if it was working since it was a warning. There was no problem with the last code."}}
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