{"action":"created","comment":{"url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/pulls/comments/25600987","id":25600987,"diff_hunk":"@@ -63,34 +63,36 @@ object ReportGenerator {\n    * the \"GATKText.properties\" file and used that as the version of GATK.\n    */\n   private def getGATKVersion(): String = {\n-    val jars = getJarsOnClassPath()\n-    val gatkJars =\n-      jars.filter(s => s.getName().contains(\"GenomeAnalysisTK.jar\"))\n-\n-    if (gatkJars.size == 1) {\n-      val jarFile = new JarFile(gatkJars(0).getAbsolutePath())\n-\n-      val properties = jarFile.getEntry(\"GATKText.properties\")\n-      val version =\n-        if (properties == null)\n-          Constants.unknown\n-        else {\n-          val inputStream = jarFile.getInputStream(properties)\n-\n-          val reader = scala.io.Source.fromInputStream(inputStream)\n-          val versionLine =\n-            reader.getLines.find(p =>\n-              p.startsWith(\"org.broadinstitute.gatk.engine.CommandLineGATK.version=\"))\n-          val versionFromFile = versionLine.getOrElse(Constants.unknown).split(\"=\")(1)\n-\n-          reader.close\n-          inputStream.close()\n-\n-          versionFromFile\n-        }\n-      version\n-    } else\n-      Constants.unknown\n+//    val jars = getJarsOnClassPath()\n+//    val gatkJars =\n+//      jars.filter(s => s.getName().contains(\"Queue.jar\"))\n+//\n+//    if (gatkJars.size == 1) {\n+//      val jarFile = new JarFile(gatkJars(0).getAbsolutePath())\n+//\n+//      val properties = jarFile.getEntry(\"GATKText.properties\")\n+//      val version =\n+//        if (properties == null)\n+//          Constants.unknown\n+//        else {\n+//          val inputStream = jarFile.getInputStream(properties)\n+//\n+//          val reader = scala.io.Source.fromInputStream(inputStream)\n+//          val versionLine =\n+//            reader.getLines.find(p =>\n+//              p.startsWith(\"org.broadinstitute.gatk.engine.CommandLineGATK.version=\"))\n+//          val versionFromFile = versionLine.getOrElse(Constants.unknown).split(\"=\")(1)\n+//\n+//          reader.close\n+//          inputStream.close()\n+//\n+//          versionFromFile\n+//        }\n+//      version\n+//    } else\n+//      Constants.unknown\n+    org.broadinstitute.gatk.engine.CommandLineGATK.getVersionNumber","path":"src/main/scala/molmed/report/ReportGenerator.scala","position":60,"original_position":60,"commit_id":"0c52c762c8cfe9f495c5ac3783f62c5af2c25b5f","original_commit_id":"0c52c762c8cfe9f495c5ac3783f62c5af2c25b5f","user":{"login":"biocyberman","id":447942,"avatar_url":"https://avatars.githubusercontent.com/u/447942?v=3","gravatar_id":"","url":"https://api.github.com/users/biocyberman","html_url":"https://github.com/biocyberman","followers_url":"https://api.github.com/users/biocyberman/followers","following_url":"https://api.github.com/users/biocyberman/following{/other_user}","gists_url":"https://api.github.com/users/biocyberman/gists{/gist_id}","starred_url":"https://api.github.com/users/biocyberman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocyberman/subscriptions","organizations_url":"https://api.github.com/users/biocyberman/orgs","repos_url":"https://api.github.com/users/biocyberman/repos","events_url":"https://api.github.com/users/biocyberman/events{/privacy}","received_events_url":"https://api.github.com/users/biocyberman/received_events","type":"User","site_admin":false},"body":"Hehe, I found it by chance when I was trying to remove dependency for GenomeAnalysisTK.jar. The key is that I knew we don't kneed Queue.jar and GenomeAnalaysisTK..jar to run `piper`.","created_at":"2015-03-02T14:23:59Z","updated_at":"2015-03-02T14:23:59Z","html_url":"https://github.com/NationalGenomicsInfrastructure/piper/pull/52#discussion_r25600987","pull_request_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/pulls/52","_links":{"self":{"href":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/pulls/comments/25600987"},"html":{"href":"https://github.com/NationalGenomicsInfrastructure/piper/pull/52#discussion_r25600987"},"pull_request":{"href":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/pulls/52"}}},"pull_request":{"url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/pulls/52","id":29056417,"html_url":"https://github.com/NationalGenomicsInfrastructure/piper/pull/52","diff_url":"https://github.com/NationalGenomicsInfrastructure/piper/pull/52.diff","patch_url":"https://github.com/NationalGenomicsInfrastructure/piper/pull/52.patch","issue_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/issues/52","number":52,"state":"open","locked":false,"title":"To allow institution-specific setup","user":{"login":"biocyberman","id":447942,"avatar_url":"https://avatars.githubusercontent.com/u/447942?v=3","gravatar_id":"","url":"https://api.github.com/users/biocyberman","html_url":"https://github.com/biocyberman","followers_url":"https://api.github.com/users/biocyberman/followers","following_url":"https://api.github.com/users/biocyberman/following{/other_user}","gists_url":"https://api.github.com/users/biocyberman/gists{/gist_id}","starred_url":"https://api.github.com/users/biocyberman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocyberman/subscriptions","organizations_url":"https://api.github.com/users/biocyberman/orgs","repos_url":"https://api.github.com/users/biocyberman/repos","events_url":"https://api.github.com/users/biocyberman/events{/privacy}","received_events_url":"https://api.github.com/users/biocyberman/received_events","type":"User","site_admin":false},"body":"I would like to suggest merging of the following two commits:\r\n\r\n**Commit aac74bce7e22**\r\n\r\nhttps://github.com/biocyberman/piper/commit/aac74bce7e22137e6fb7a539f21102c7ef5ebf3e\r\n\r\nI created a 'config' directory at project base and moved three original files to 'config/upsala': `globalConfig.sh globalConfig.xml uppmax_global_config.xml`. I then modified `setup.sh` file to allow this syntax: \r\n\r\n`./setup.sh /path/to/install/piper institution /path/to/otherlibraries/lib NoGATKCompile`\r\n\r\nAn example command is like this: `./setup.sh /space/system/piper afmd /space/system/lib nogatk`\r\n\r\nWhich means:\r\n\r\n1. To install piper to ` /space/system/piper`\r\n2. To pickup config files under `config/afmd` directory. Current possible choices are `afmd` and `upsala`, but more subdirectories for any new institutions can be added.\r\n3. Register /space/system/lib to piper so it can look for additional library dependencies (If they are put there, of course)\r\n4. The fourth argument, whenever none-empty, will tell `setup.sh` not to download and compile GATK. This is nicer than commenting/uncommenting the function call.\r\n\r\n\r\n**Commit 704a1ac9d26cc686d** \r\nThis is an additional commit to remove dependency on `GenomeAnalysisTK.jar`. This is because `Queue.jar` already includes content of `GenomeAnalysisTK.jar`. Putting both of them together in `lib` causes warning about redundant packages found, such as the one about `org.slf4j` bindings.\r\n\r\nhttps://github.com/biocyberman/piper/commit/704a1ac9d26cc686d460fd93dc9b551f6ced77f5\r\n\r\nMy commit tree looks a bit messy, I will try to keep them in good order from now on :)\r\n\r\n","created_at":"2015-02-10T23:40:36Z","updated_at":"2015-03-02T14:24:00Z","closed_at":null,"merged_at":null,"merge_commit_sha":null,"assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/pulls/52/commits","review_comments_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/pulls/52/comments","review_comment_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/pulls/comments{/number}","comments_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/issues/52/comments","statuses_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/piper/statuses/0c52c762c8cfe9f495c5ac3783f62c5af2c25b5f","head":{"label":"biocyberman:QPipe","ref":"QPipe","sha":"0c52c762c8cfe9f495c5ac3783f62c5af2c25b5f","user":{"login":"biocyberman","id":447942,"avatar_url":"https://avatars.githubusercontent.com/u/447942?v=3","gravatar_id":"","url":"https://api.github.com/users/biocyberman","html_url":"https://github.com/biocyberman","followers_url":"https://api.github.com/users/biocyberman/followers","following_url":"https://api.github.com/users/biocyberman/following{/other_user}","gists_url":"https://api.github.com/users/biocyberman/gists{/gist_id}","starred_url":"https://api.github.com/users/biocyberman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocyberman/subscriptions","organizations_url":"https://api.github.com/users/biocyberman/orgs","repos_url":"https://api.github.com/users/biocyberman/repos","events_url":"https://api.github.com/users/biocyberman/events{/privacy}","received_events_url":"https://api.github.com/users/biocyberman/received_events","type":"User","site_admin":false},"repo":{"id":29482640,"name":"piper","full_name":"biocyberman/piper","owner":{"login":"biocyberman","id":447942,"avatar_url":"https://avatars.githubusercontent.com/u/447942?v=3","gravatar_id":"","url":"https://api.github.com/users/biocyberman","html_url":"https://github.com/biocyberman","followers_url":"https://api.github.com/users/biocyberman/followers","following_url":"https://api.github.com/users/biocyberman/following{/other_user}","gists_url":"https://api.github.com/users/biocyberman/gists{/gist_id}","starred_url":"https://api.github.com/users/biocyberman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocyberman/subscriptions","organizations_url":"https://api.github.com/users/biocyberman/orgs","repos_url":"https://api.github.com/users/biocyberman/repos","events_url":"https://api.github.com/users/biocyberman/events{/privacy}","received_events_url":"https://api.github.com/users/biocyberman/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/biocyberman/piper","description":"A 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