{"action":"created","issue":{"url":"https://api.github.com/repos/bioboxes/data/issues/4","repository_url":"https://api.github.com/repos/bioboxes/data","labels_url":"https://api.github.com/repos/bioboxes/data/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/bioboxes/data/issues/4/comments","events_url":"https://api.github.com/repos/bioboxes/data/issues/4/events","html_url":"https://github.com/bioboxes/data/issues/4","id":193999063,"number":4,"title":"Update bioboxes image list","user":{"login":"pbelmann","id":8780236,"avatar_url":"https://avatars.githubusercontent.com/u/8780236?v=3","gravatar_id":"","url":"https://api.github.com/users/pbelmann","html_url":"https://github.com/pbelmann","followers_url":"https://api.github.com/users/pbelmann/followers","following_url":"https://api.github.com/users/pbelmann/following{/other_user}","gists_url":"https://api.github.com/users/pbelmann/gists{/gist_id}","starred_url":"https://api.github.com/users/pbelmann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pbelmann/subscriptions","organizations_url":"https://api.github.com/users/pbelmann/orgs","repos_url":"https://api.github.com/users/pbelmann/repos","events_url":"https://api.github.com/users/pbelmann/events{/privacy}","received_events_url":"https://api.github.com/users/pbelmann/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-12-07T09:32:47Z","updated_at":"2016-12-08T11:48:33Z","closed_at":null,"body":"I suggest the following changes:\r\n\r\n1.\r\n\r\n**Problem:** One tool/image could implement multiple interfaces. By using the current list we would have to list the an image for each interface. \r\n\r\n**Solution:** in PR #2  I suggest to change the list to the following format where we state for each task the corresponding interface:\r\n\r\n~~~BASH\r\n    title: velvet\r\n    image:\r\n      dockerhub: bioboxes/velvet\r\n      repo: https://github.com/bioboxes/velvet\r\n      source: https://github.com/dzerbino/velvet\r\n    pmid: 18349386\r\n    homepage: https://www.ebi.ac.uk/~zerbino/velvet/\r\n    mailing_list: http://listserver.ebi.ac.uk/mailman/listinfo/velvet-users\r\n    description:\r\n      The velvet assembler was one of the first assemblers created for short read sequencing. Velvet was developed at the European Bioinformatics Institute.\r\n    tasks:\r\n      - name: default\r\n        interface: assembler\r\n      - name: careful\r\n        interface: assembler\r\n~~~\r\n\r\nInterfaces are listed in a separate file: [interfaces.yml](https://github.com/pbelmann/data/blob/feature/new-image-list/interfaces.yml)\r\n\r\n2. @michaelbarton  suggested to add SHA ids of the bioboxes images.\r\n\r\n3. I suggest to add a field called 'tags'. This field should allow us to add categories for each biobox.\r\n\r\nExample:   \r\n\r\n~~~BASH\r\n    title: ray\r\n    image:\r\n      dockerhub: bioboxes/ray\r\n      repo: https://github.com/sebhtml/ray\r\n      source:\r\n    pmid: 20958248\r\n    homepage: http://gatb.inria.fr/\r\n    tags: [nucleotid.es, CAMI]\r\n    mailing_list: https://www.biostars.org/t/gatb/\r\n    description: \r\n      Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.\r\n    tasks:\r\n      - name: default\r\n        interface: assembler\r\n~~~\r\n\r\n4. @fernandomeyer  added the velour biobox but our [page](http://bioboxes.org/available-bioboxes/) on bioboxes.org is not updated. Maybe we should implement this listing by using javascript which allows us to fetch the list each time the webpage is opened.\r\n\r\n\r\n "},"comment":{"url":"https://api.github.com/repos/bioboxes/data/issues/comments/265722130","html_url":"https://github.com/bioboxes/data/issues/4#issuecomment-265722130","issue_url":"https://api.github.com/repos/bioboxes/data/issues/4","id":265722130,"user":{"login":"pbelmann","id":8780236,"avatar_url":"https://avatars.githubusercontent.com/u/8780236?v=3","gravatar_id":"","url":"https://api.github.com/users/pbelmann","html_url":"https://github.com/pbelmann","followers_url":"https://api.github.com/users/pbelmann/followers","following_url":"https://api.github.com/users/pbelmann/following{/other_user}","gists_url":"https://api.github.com/users/pbelmann/gists{/gist_id}","starred_url":"https://api.github.com/users/pbelmann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pbelmann/subscriptions","organizations_url":"https://api.github.com/users/pbelmann/orgs","repos_url":"https://api.github.com/users/pbelmann/repos","events_url":"https://api.github.com/users/pbelmann/events{/privacy}","received_events_url":"https://api.github.com/users/pbelmann/received_events","type":"User","site_admin":false},"created_at":"2016-12-08T11:48:33Z","updated_at":"2016-12-08T11:48:33Z","body":"> > **Problem:** One tool/image could implement multiple interfaces. By using the\r\ncurrent list we would have to list the an image for each interface.\r\n\r\n> My preference is for each biobox is to implement one type of interface to\r\nsimplify the management of biobox images, especially the image tasks. Having\r\none interface per biobox image means that each of the task is scoped by the\r\ninterface too. For example the `default` task for assembler should imply the\r\nwhat the author belives is the best possible assembly given a wide variety of\r\ninputs, which is what the CLI runs if `--task` is not specified. A careful\r\ntask implies trading assembly size for accuracy.\r\n\r\nI agree this would be difficult if we want to specify a default task for each interface. \r\nIn CAMI we have for example binning evaluation tools that could be used taxonomic and non taxonomic binning files. Thats why they implement the taxonomic and non-taxonomic binning evaluation interface.\r\nBut I guess we will have to build two different images that are fetching the same library/github repository. \r\n\r\n>I have been using SHA256 digests so far because this is supported\r\nby the docker client. For example the command:\r\ndocker run repo/image@sha256:digest\r\n\r\nOk, so using or listing the digest does makes sense if you are referencing a specific biobox from a different service, like nucleotid.es or CAMI.\r\n\r\n>I think the tags you mentioned refer to a different use case though, is\r\nthat correct?\r\n\r\nYes, with tags I do not mean docker tags. I think it would be useful in our current bioboxes listing (http://bioboxes.org/available-bioboxes/) to have a field called 'tags' or 'metatags'. In this field we could categorize our containers. Tags could be for example 'CAMI' or 'nucleotid.es'.\r\n\r\n>> 4. @fernandomeyer  added the velour biobox but our\r\n[page](http://bioboxes.org/available-bioboxes/) on bioboxes.org is not\r\nupdated. Maybe we should implement this listing by using javascript which\r\nallows us to fetch the list each time the webpage is opened.\r\n\r\n>I believe we could update the circle.yml for the data repository to\r\nautomatically request a rebuild of the website every time a pull request is\r\nmerged into master.\r\n\r\nSounds great! Could you update the repo? \r\n\r\n"}}
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