{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2050","repository_url":"https://api.github.com/repos/galaxyproject/galaxy","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2050/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2050/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2050/events","html_url":"https://github.com/galaxyproject/galaxy/issues/2050","id":144758702,"number":2050,"title":"bug with hidden_data?","user":{"login":"methylome","id":9466414,"avatar_url":"https://avatars.githubusercontent.com/u/9466414?v=3","gravatar_id":"","url":"https://api.github.com/users/methylome","html_url":"https://github.com/methylome","followers_url":"https://api.github.com/users/methylome/followers","following_url":"https://api.github.com/users/methylome/following{/other_user}","gists_url":"https://api.github.com/users/methylome/gists{/gist_id}","starred_url":"https://api.github.com/users/methylome/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/methylome/subscriptions","organizations_url":"https://api.github.com/users/methylome/orgs","repos_url":"https://api.github.com/users/methylome/repos","events_url":"https://api.github.com/users/methylome/events{/privacy}","received_events_url":"https://api.github.com/users/methylome/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/area/tool-framework","name":"area/tool-framework","color":"006b75"},{"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/kind/bug","name":"kind/bug","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/galaxyproject/galaxy/milestones/2","html_url":"https://github.com/galaxyproject/galaxy/milestones/16.04","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/milestones/2/labels","id":1435676,"number":2,"title":"16.04","description":"Tentative freeze date for 16.04","creator":{"login":"erasche","id":458683,"avatar_url":"https://avatars.githubusercontent.com/u/458683?v=3","gravatar_id":"","url":"https://api.github.com/users/erasche","html_url":"https://github.com/erasche","followers_url":"https://api.github.com/users/erasche/followers","following_url":"https://api.github.com/users/erasche/following{/other_user}","gists_url":"https://api.github.com/users/erasche/gists{/gist_id}","starred_url":"https://api.github.com/users/erasche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/erasche/subscriptions","organizations_url":"https://api.github.com/users/erasche/orgs","repos_url":"https://api.github.com/users/erasche/repos","events_url":"https://api.github.com/users/erasche/events{/privacy}","received_events_url":"https://api.github.com/users/erasche/received_events","type":"User","site_admin":false},"open_issues":9,"closed_issues":217,"state":"open","created_at":"2015-11-30T17:22:37Z","updated_at":"2016-04-05T17:33:15Z","due_on":"2016-04-06T04:00:00Z","closed_at":null},"comments":16,"created_at":"2016-03-31T00:57:13Z","updated_at":"2016-04-05T18:18:03Z","closed_at":null,"body":"https://github.com/galaxyproject/tools-devteam/issues/341\r\nIn release 16_01, devteam's cufflinks 2.2.1.0 was failed and I guess it's caused by a galaxy's bug with hidden_data. Actually I can't find how hidden_data is set.\r\n\r\nIn cufflinks_wrapper.xml, the following code \r\n...\r\n`            ## Include reference annotation?`\r\n`            #if $reference_annotation.use_ref == \"Use reference annotation\":`\r\n`                -G $reference_annotation.reference_annotation_file`\r\n`                $reference_annotation.compatible_hits_norm`\r\n`            #end if`\r\n`            #if $reference_annotation.use_ref == \"Use reference annotation guide\":`\r\n`                -g $reference_annotation.reference_annotation_guide_file`\r\n`                --3-overhang-tolerance=$reference_annotation.three_overhang_tolerance`\r\n`                --intron-overhang-tolerance=$reference_annotation.intron_overhang_tolerance`\r\n`                $reference_annotation.no_faux_reads`\r\n`            #end if`\r\n`...`\r\n`            ## Include global model if available.`\r\n`            #if $global_model:`\r\n`                --global_model=$global_model`\r\n`            #end if`\r\n`...`\r\n`        <param name=\"global_model\" type=\"hidden_data\" label=\"Global model (for use in Trackster)\" optional=\"True\"/>`\r\n\r\ngenerated the following in tool_script.sh where `$global_model` is set to the value of `$reference_annotation.reference_annotation_guide_file`.\r\n\r\n`python /home/galaxy/dev/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/64698e16f4a6/cufflinks/cufflinks_wrapper.py --input=/home/galaxy/dev/database/files/000/dataset_634.dat --assembled-isoforms-output=/home/galaxy/dev/database/files/000/dataset_654.dat --num-threads=\"${GALAXY_SLOTS:-4}\" -I 300000 -F 0.1 -j 0.15   -g /home/galaxy/dev/database/files/000/dataset_26.dat --3-overhang-tolerance=600 --intron-overhang-tolerance=50   -b --ref_file=/data/hg19/hg19dip.fa  -u  --global_model=/home/galaxy/dev/database/files/000/dataset_26.dat`"},"comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments/205928208","html_url":"https://github.com/galaxyproject/galaxy/issues/2050#issuecomment-205928208","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/2050","id":205928208,"user":{"login":"mvdbeek","id":6804901,"avatar_url":"https://avatars.githubusercontent.com/u/6804901?v=3","gravatar_id":"","url":"https://api.github.com/users/mvdbeek","html_url":"https://github.com/mvdbeek","followers_url":"https://api.github.com/users/mvdbeek/followers","following_url":"https://api.github.com/users/mvdbeek/following{/other_user}","gists_url":"https://api.github.com/users/mvdbeek/gists{/gist_id}","starred_url":"https://api.github.com/users/mvdbeek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvdbeek/subscriptions","organizations_url":"https://api.github.com/users/mvdbeek/orgs","repos_url":"https://api.github.com/users/mvdbeek/repos","events_url":"https://api.github.com/users/mvdbeek/events{/privacy}","received_events_url":"https://api.github.com/users/mvdbeek/received_events","type":"User","site_admin":false},"created_at":"2016-04-05T18:18:03Z","updated_at":"2016-04-05T18:18:03Z","body":"@methylome just for reference, you're not using [this patch](https://github.com/galaxyproject/tools-iuc/issues/631#issuecomment-191254337) anymore? It shouldn't hurt, but it's better to be on release_16.01 which has a better solution for that problem.\r\n\r\nAlso, can you give us the output of `git status` and `git branch -v` ?"}}