{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/491","repository_url":"https://api.github.com/repos/galaxyproject/tools-devteam","labels_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/491/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/491/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/491/events","html_url":"https://github.com/galaxyproject/tools-devteam/issues/491","id":264171612,"number":491,"title":"FastQC: fonts problem","user":{"login":"bernt-matthias","id":25689525,"avatar_url":"https://avatars1.githubusercontent.com/u/25689525?v=4","gravatar_id":"","url":"https://api.github.com/users/bernt-matthias","html_url":"https://github.com/bernt-matthias","followers_url":"https://api.github.com/users/bernt-matthias/followers","following_url":"https://api.github.com/users/bernt-matthias/following{/other_user}","gists_url":"https://api.github.com/users/bernt-matthias/gists{/gist_id}","starred_url":"https://api.github.com/users/bernt-matthias/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bernt-matthias/subscriptions","organizations_url":"https://api.github.com/users/bernt-matthias/orgs","repos_url":"https://api.github.com/users/bernt-matthias/repos","events_url":"https://api.github.com/users/bernt-matthias/events{/privacy}","received_events_url":"https://api.github.com/users/bernt-matthias/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-10-10T10:11:44Z","updated_at":"2017-10-11T08:31:28Z","closed_at":null,"author_association":"NONE","body":"When running FastQC (latest tool version) I get the following error (after which the FastQC java application is idling around). \r\n\r\nThe used `-Djava.awt.headless=true` parameter is one suggested solution: \r\nhttps://stackoverflow.com/questions/4438839/java-on-debian-probable-fatal-error-no-fonts-found\r\nbut seems not to work here (centos). Often missing dejavu and and bitmap dependencies are discussed. \r\n\r\n```\r\njava.lang.Error: Probable fatal error:No fonts found.\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1236)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1100)\r\n\tat sun.font.SunFontManager.findOtherDeferredFont(SunFontManager.java:1037)\r\n\tat sun.font.SunFontManager.findDeferredFont(SunFontManager.java:1054)\r\n\tat sun.font.SunFontManager.findFont2D(SunFontManager.java:2256)\r\n\tat sun.font.SunFontManager.getDefaultPhysicalFont(SunFontManager.java:1220)\r\n\tat sun.font.SunFontManager.initialiseDeferredFont(SunFontManager.java:1106)\r\n\tat sun.font.CompositeFont.doDeferredInitialisation(CompositeFont.java:263)\r\n\tat sun.font.CompositeFont.getSlotFont(CompositeFont.java:352)\r\n\tat sun.font.CompositeStrike.getStrikeForSlot(CompositeStrike.java:78)\r\n\tat sun.font.CompositeStrike.getFontMetrics(CompositeStrike.java:93)\r\n\tat sun.font.FontDesignMetrics.initMatrixAndMetrics(FontDesignMetrics.java:359)\r\n\tat sun.font.FontDesignMetrics.<init>(FontDesignMetrics.java:350)\r\n\tat sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:302)\r\n\tat sun.java2d.SunGraphics2D.getFontMetrics(SunGraphics2D.java:855)\r\n\tat uk.ac.babraham.FastQC.Graphs.QualityBoxPlot.paint(QualityBoxPlot.java:88)\r\n\tat javax.swing.JComponent.print(JComponent.java:1202)\r\n\tat uk.ac.babraham.FastQC.Modules.AbstractQCModule.writeDefaultImage(AbstractQCModule.java:68)\r\n\tat uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.makeReport(PerBaseQualityScores.java:199)\r\n\tat uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:131)\r\n\tat uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:155)\r\n\tat uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)\r\n\tat java.lang.Thread.run(Thread.java:745)\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/comments/335732994","html_url":"https://github.com/galaxyproject/tools-devteam/issues/491#issuecomment-335732994","issue_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/491","id":335732994,"user":{"login":"bernt-matthias","id":25689525,"avatar_url":"https://avatars1.githubusercontent.com/u/25689525?v=4","gravatar_id":"","url":"https://api.github.com/users/bernt-matthias","html_url":"https://github.com/bernt-matthias","followers_url":"https://api.github.com/users/bernt-matthias/followers","following_url":"https://api.github.com/users/bernt-matthias/following{/other_user}","gists_url":"https://api.github.com/users/bernt-matthias/gists{/gist_id}","starred_url":"https://api.github.com/users/bernt-matthias/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bernt-matthias/subscriptions","organizations_url":"https://api.github.com/users/bernt-matthias/orgs","repos_url":"https://api.github.com/users/bernt-matthias/repos","events_url":"https://api.github.com/users/bernt-matthias/events{/privacy}","received_events_url":"https://api.github.com/users/bernt-matthias/received_events","type":"User","site_admin":false},"created_at":"2017-10-11T08:31:28Z","updated_at":"2017-10-11T08:31:28Z","author_association":"NONE","body":"The only openjdk related files that I find with `find /gpfs1/data/galaxy_server/galaxy/database/dependencies/_conda/envs/__fastqc@0.11.5/ -iname \"*open*\"` is `./openjdk-8.0.121-1.json`\r\n\r\nBut the used `java` seems to be openjdk:\r\n\r\n`/gpfs1/data/galaxy_server/galaxy/database/dependencies/_conda/envs/__fastqc@0.11.5/bin/java -version`\r\n\r\n```\r\nopenjdk version \"1.8.0_121\"\r\nOpenJDK Runtime Environment (Zulu 8.20.0.5-linux64) (build 1.8.0_121-b15)\r\nOpenJDK 64-Bit Server VM (Zulu 8.20.0.5-linux64) (build 25.121-b15, mixed mode)\r\n```"}}
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