{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/19","repository_url":"https://api.github.com/repos/COMBINE-lab/salmon","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/19/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/19/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/19","id":109233280,"number":19,"title":"upgrade CMakeLists.txt to use external copies of dependencies & no downloading","user":{"login":"mr-c","id":1330696,"avatar_url":"https://avatars.githubusercontent.com/u/1330696?v=3","gravatar_id":"","url":"https://api.github.com/users/mr-c","html_url":"https://github.com/mr-c","followers_url":"https://api.github.com/users/mr-c/followers","following_url":"https://api.github.com/users/mr-c/following{/other_user}","gists_url":"https://api.github.com/users/mr-c/gists{/gist_id}","starred_url":"https://api.github.com/users/mr-c/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mr-c/subscriptions","organizations_url":"https://api.github.com/users/mr-c/orgs","repos_url":"https://api.github.com/users/mr-c/repos","events_url":"https://api.github.com/users/mr-c/events{/privacy}","received_events_url":"https://api.github.com/users/mr-c/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-10-01T05:36:37Z","updated_at":"2016-03-11T17:01:57Z","closed_at":null,"body":"Hello!\r\n\r\nI'm packaging salmon and many of its dependencies for Debian in support of https://github.com/Blahah/transrate/issues/160\r\n\r\nI have a messy patch to enable the use of external libraries instead of bundled or downloaded copies at http://anonscm.debian.org/cgit/debian-med/salmon.git/plain/debian/patches/dependency-fix\r\n\r\nAs I'm not a CMake expert I was only able to make it work for Debian instead of a generic solution that would fall back to the shipped copies or downloading as it is now.\r\n\r\nPerhaps you all are better with CMake than I am? A generic solution would be best so I don't have to adjust the patch with every change to the CMakeLists.txt\r\n\r\nSpecifically it would be great to support\r\n- [ ] external copy of spdlog headers and the cereal serialization headers\r\n- linking to external dynamic libraries for\r\n  - [ ] boost\r\n    - Headers: https://packages.debian.org/sid/amd64/libboost1.58-dev/filelist\r\n    - Sample library layout: https://packages.debian.org/sid/amd64/libboost-filesystem1.58-dev/filelist\r\n  - [ ] bwa\r\n    - Headers & library: https://ftp-master.debian.org/new/bwa_0.7.12-5.html\r\n  - [ ] jellyfish\r\n    - Headers & library: https://packages.debian.org/sid/amd64/libjellyfish-2.0-dev/filelist\r\n  - [ ] tbb\r\n    - Headers & library: https://packages.debian.org/sid/amd64/libtbb-dev/filelist\r\n  - [ ] libgff\r\n    - Headers & library: https://ftp-master.debian.org/new/libgff_1.0-1.html\r\n  - [ ] staden IOLib\r\n    - Headers & library: https://packages.debian.org/sid/amd64/libstaden-read-dev/filelist\r\n\r\nI also have a patch to support the latest release of jellyfish that I can turn into a pull request, should you want it: http://anonscm.debian.org/cgit/debian-med/salmon.git/plain/debian/patches/jellyfish-update\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/comments/195454798","html_url":"https://github.com/COMBINE-lab/salmon/issues/19#issuecomment-195454798","issue_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/19","id":195454798,"user":{"login":"sjackman","id":291551,"avatar_url":"https://avatars.githubusercontent.com/u/291551?v=3","gravatar_id":"","url":"https://api.github.com/users/sjackman","html_url":"https://github.com/sjackman","followers_url":"https://api.github.com/users/sjackman/followers","following_url":"https://api.github.com/users/sjackman/following{/other_user}","gists_url":"https://api.github.com/users/sjackman/gists{/gist_id}","starred_url":"https://api.github.com/users/sjackman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjackman/subscriptions","organizations_url":"https://api.github.com/users/sjackman/orgs","repos_url":"https://api.github.com/users/sjackman/repos","events_url":"https://api.github.com/users/sjackman/events{/privacy}","received_events_url":"https://api.github.com/users/sjackman/received_events","type":"User","site_admin":false},"created_at":"2016-03-11T17:01:57Z","updated_at":"2016-03-11T17:01:57Z","body":"As a user, I prefer autotools to cmake. cmake breaks way more often in my hands/experience than autotools. As a developer, I've only used autotools, so my previous opinion is probably biased."}}