{"action":"created","issue":{"url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/574","labels_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/574/labels{/name}","comments_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/574/comments","events_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/574/events","html_url":"https://github.com/bioconda/bioconda-recipes/pull/574","id":125613529,"number":574,"title":"add R packages from the Galaxy TS","user":{"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},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-01-08T13:30:02Z","updated_at":"2016-01-08T15:06:09Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/bioconda/bioconda-recipes/pulls/574","html_url":"https://github.com/bioconda/bioconda-recipes/pull/574","diff_url":"https://github.com/bioconda/bioconda-recipes/pull/574.diff","patch_url":"https://github.com/bioconda/bioconda-recipes/pull/574.patch"},"body":""},"comment":{"url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/comments/170026392","html_url":"https://github.com/bioconda/bioconda-recipes/pull/574#issuecomment-170026392","issue_url":"https://api.github.com/repos/bioconda/bioconda-recipes/issues/574","id":170026392,"user":{"login":"daler","id":115406,"avatar_url":"https://avatars.githubusercontent.com/u/115406?v=3","gravatar_id":"","url":"https://api.github.com/users/daler","html_url":"https://github.com/daler","followers_url":"https://api.github.com/users/daler/followers","following_url":"https://api.github.com/users/daler/following{/other_user}","gists_url":"https://api.github.com/users/daler/gists{/gist_id}","starred_url":"https://api.github.com/users/daler/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/daler/subscriptions","organizations_url":"https://api.github.com/users/daler/orgs","repos_url":"https://api.github.com/users/daler/repos","events_url":"https://api.github.com/users/daler/events{/privacy}","received_events_url":"https://api.github.com/users/daler/received_events","type":"User","site_admin":false},"created_at":"2016-01-08T15:06:09Z","updated_at":"2016-01-08T15:06:09Z","body":"Ah, I see. Is the `rjson` dependency you mention an additional dependency required by Galaxy? That is, is this a patched version of DESeq2 that only Galaxy would use, or is it the default v1.8.2?\r\n\r\nIf the latter, can the recipe go in older-version-subdirectories as you've done in the other parts of the migration you're doing? That way others could easily find the older DESeq2 versions without having to know they need to add the `gx` tag to get the older version.\r\n\r\nI guess it boils down either wgetting all specific dependencies in the `gx-deseq2` package's `build.sh` for a version that only Galaxy would use, or creating all the older dependency recipes for general use from bioconda. As long as these older dependencies are standard bioconductor packages and not patched specifically for Galaxy, I think the latter might be better. For example, how many of the Galaxy recipes depend on IRanges? Might as well have a conda recipe for it for speedy package building and use by other packages.\r\n\r\nBut, as you mention, you need to be able to pin versions in the bioconductor recipe scripts to make this work easily. This would be a really helpful feature and it should be simple to add. If a version is specified on the command line, the skeleton script can grab it directly from bioaRchive (as long as that version is available)."}}