{"action":"created","issue":{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/25","repository_url":"https://api.github.com/repos/openjournals/joss-reviews","labels_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/25/comments","events_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/25/events","html_url":"https://github.com/openjournals/joss-reviews/issues/25","id":157420483,"number":25,"title":"Submission: GeneNetwork: framework for web-based genetics","user":{"login":"whedon","id":18508068,"avatar_url":"https://avatars.githubusercontent.com/u/18508068?v=3","gravatar_id":"","url":"https://api.github.com/users/whedon","html_url":"https://github.com/whedon","followers_url":"https://api.github.com/users/whedon/followers","following_url":"https://api.github.com/users/whedon/following{/other_user}","gists_url":"https://api.github.com/users/whedon/gists{/gist_id}","starred_url":"https://api.github.com/users/whedon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/whedon/subscriptions","organizations_url":"https://api.github.com/users/whedon/orgs","repos_url":"https://api.github.com/users/whedon/repos","events_url":"https://api.github.com/users/whedon/events{/privacy}","received_events_url":"https://api.github.com/users/whedon/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openjournals/joss-reviews/labels/review","name":"review","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":10,"created_at":"2016-05-30T02:17:29Z","updated_at":"2016-06-02T09:01:59Z","closed_at":null,"body":"**Submitting author:** @pjotrp (<a href=\"http://orcid.org/0000-0002-8021-9162\">Pjotr Prins</a>)\r\n**Repository:** <a href=\"https://github.com/genenetwork/genenetwork2\" target =\"_blank\">https://github.com/genenetwork/genenetwork2</a>\r\n**Version:** 2.0-a8fcff4\r\n**Archive:** <a href=\"http://dx.doi.org/10.5281/zenodo.53740\" target =\"_blank\">10.5281/zenodo.53740</a>\r\n\r\n## Status\r\n\r\n[![status](http://joss.theoj.org/papers/84b27b28948be80a47268a5baa2701ad/status.svg)](http://joss.theoj.org/papers/84b27b28948be80a47268a5baa2701ad)\r\n\r\nStatus badge code:\r\n\r\n```\r\nHTML: <a href=\"http://joss.theoj.org/papers/84b27b28948be80a47268a5baa2701ad\"><img src=\"http://joss.theoj.org/papers/84b27b28948be80a47268a5baa2701ad/status.svg\"></a>\r\nMarkdown: [![status](http://joss.theoj.org/papers/84b27b28948be80a47268a5baa2701ad/status.svg)](http://joss.theoj.org/papers/84b27b28948be80a47268a5baa2701ad)\r\n```\r\n\r\n## Reviewer questions\r\n\r\n### Conflict of interest\r\n\r\n- [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).  \r\n\r\n### General checks\r\n\r\n- [x] **Repository:** Is the source code for this software available at the <a target=\"_blank\" href=\"https://github.com/genenetwork/genenetwork2\">repository url</a>?\r\n- [x] **License:** Does the repository contain a plain-text LICENSE file with the contents of an [OSI approved](https://opensource.org/licenses/alphabetical) software license?\r\n- [x] **Version:** Does the release version given match the GitHub release (2.0-a8fcff4)?\r\n- [x] **Archive:** Does the <a target=\"_blank\" href=\"http://dx.doi.org/10.5281/zenodo.53740\">software archive</a> resolve?\r\n\r\n### Functionality\r\n\r\n- [ ] **Installation:** Does installation proceed as outlined in the documentation?\r\n- [ ] **Functionality:** Have the functional claims of the software been confirmed?\r\n- [ ] **Performance:** Have the performance claims of the software been confirmed?\r\n\r\n### Documentation\r\n\r\n- [x] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [x] **Installation instructions:** Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.\r\n- [ ] **Example usage:** Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).\r\n- [ ] **Functionality documentation:** Is the functionality of the software documented to a satisfactory level (e.g. API method documentation)?\r\n- [x] **Automated tests:** Are there automated tests or manual steps described so that the function of the software can be verified?\r\n- [x] **Community guidelines:** Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support\r\n\r\n### Software paper\r\n\r\nPaper PDF: [10.21105.joss.00025.pdf](https://github.com/openjournals/joss-reviews/files/288706/10.21105.joss.00025.pdf)\r\n\r\n- [x] **Authors:** Does the `paper.md` file include a list of authors with their affiliations?\r\n- [x] **A statement of need:** Do the authors clearly state what problems the software is designed to solve and who the target audience is?\r\n- [x] **References:** Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?\r\n"},"comment":{"url":"https://api.github.com/repos/openjournals/joss-reviews/issues/comments/223235388","html_url":"https://github.com/openjournals/joss-reviews/issues/25#issuecomment-223235388","issue_url":"https://api.github.com/repos/openjournals/joss-reviews/issues/25","id":223235388,"user":{"login":"pjotrp","id":13551,"avatar_url":"https://avatars.githubusercontent.com/u/13551?v=3","gravatar_id":"","url":"https://api.github.com/users/pjotrp","html_url":"https://github.com/pjotrp","followers_url":"https://api.github.com/users/pjotrp/followers","following_url":"https://api.github.com/users/pjotrp/following{/other_user}","gists_url":"https://api.github.com/users/pjotrp/gists{/gist_id}","starred_url":"https://api.github.com/users/pjotrp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pjotrp/subscriptions","organizations_url":"https://api.github.com/users/pjotrp/orgs","repos_url":"https://api.github.com/users/pjotrp/repos","events_url":"https://api.github.com/users/pjotrp/events{/privacy}","received_events_url":"https://api.github.com/users/pjotrp/received_events","type":"User","site_admin":false},"created_at":"2016-06-02T09:01:59Z","updated_at":"2016-06-02T09:01:59Z","body":"@krother and @agarie: when it comes to installation, GN2 installation reflects that it is a rather complex product with a huge number of dependencies. It includes a recent R with packages. It includes Python with packages. It includes C++ modules. It will include OpenCL dependencies soon. Even so, GNU Guix provides a *reliable* byte-identical installation path with source *and* binary deployment. \r\n\r\nIf GN2 was part of the GNU Guix project proper it would simply be one command:\r\n\r\n```sh\r\nguix package -i genenetwork2\r\n```\r\nand all software would be installed on any Linux. \r\n\r\nUnfortunately genenetwork2 will never make it into GNU Guix. This is because some software components are dated (one python package had the last update in the 90s!) and we include large data files. \r\n\r\nGuix, however, allows you to pull in your own packages using a GUIX_PACKAGE_PATH, so we created a git repo for that named https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest (the gn-latest branch is the one we deploy).\r\n\r\nAdditionally, to ascertain byte-identical deployment we also have to fixate the GNU Guix package tree itself. This is done in yet another git repository named https://github.com/genenetwork/guix/tree/gn-latest (again the gn-latest branch).\r\n\r\nTo run these trees, after instaling GNU Guix itself, some environment variables need to be set properly\r\nand the test database has to be added to whatever mysql daemon is running.\r\n\r\nThis is all described in the installation docs as a step-by-step instruction, but I am just giving the overview here to explain why it is non-trivial at this point. Even so it *is* a formal deployment path and we and others *have* successfully installed GN2 and are happily developing against it. We include the IRC log to show it is doable - I would like to keep it there until we have a single install command. To achieve the latter we are working with the GNU Guix project to make installation easier.\r\n\r\nI am not sure the reviewers want to go through the full installation (the website also runs online), but if you do, please tell me where you are stuck and we will resolve it. It is also an opportunity for me to improve the docs ;). One thing you may gain in this process: GNU Guix is a great way of deploying bioinformatics software!\r\n\r\nTo make things easier we could deploy GN2 inside a Docker container, but we don't think that is the right way of going about deployment. Docker containers are opaque and a security risk."}}
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