{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/744","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/744/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/744/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/744/events","html_url":"https://github.com/galaxyproject/galaxy/issues/744","id":107061644,"number":744,"title":"fix 2 failing -framework tests in test_toolbox.py","user":{"login":"martenson","id":1814954,"avatar_url":"https://avatars.githubusercontent.com/u/1814954?v=3","gravatar_id":"","url":"https://api.github.com/users/martenson","html_url":"https://github.com/martenson","followers_url":"https://api.github.com/users/martenson/followers","following_url":"https://api.github.com/users/martenson/following{/other_user}","gists_url":"https://api.github.com/users/martenson/gists{/gist_id}","starred_url":"https://api.github.com/users/martenson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/martenson/subscriptions","organizations_url":"https://api.github.com/users/martenson/orgs","repos_url":"https://api.github.com/users/martenson/repos","events_url":"https://api.github.com/users/martenson/events{/privacy}","received_events_url":"https://api.github.com/users/martenson/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":{"login":"jmchilton","id":216771,"avatar_url":"https://avatars.githubusercontent.com/u/216771?v=3","gravatar_id":"","url":"https://api.github.com/users/jmchilton","html_url":"https://github.com/jmchilton","followers_url":"https://api.github.com/users/jmchilton/followers","following_url":"https://api.github.com/users/jmchilton/following{/other_user}","gists_url":"https://api.github.com/users/jmchilton/gists{/gist_id}","starred_url":"https://api.github.com/users/jmchilton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmchilton/subscriptions","organizations_url":"https://api.github.com/users/jmchilton/orgs","repos_url":"https://api.github.com/users/jmchilton/repos","events_url":"https://api.github.com/users/jmchilton/events{/privacy}","received_events_url":"https://api.github.com/users/jmchilton/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-09-17T19:55:11Z","updated_at":"2015-09-17T21:20:20Z","closed_at":null,"body":"Full log: https://jenkins.galaxyproject.org/view/Tests/job/G-framework/4/console\r\n\r\n```\r\nFAIL: output_format ( output_format ) > Test-1\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/var/lib/jenkins/jobs/G-framework/workspace/test/functional/test_toolbox.py\", line 289, in test_tool\r\n    self.do_it( td )\r\n  File \"/var/lib/jenkins/jobs/G-framework/workspace/test/functional/test_toolbox.py\", line 73, in do_it\r\n    raise e\r\nJobOutputsError: Dataset metadata verification for [file_ext] failed, expected [fastqsolexa] but found [fastqsanger].\r\n```\r\n\r\n```\r\n======================================================================\r\nFAIL: output_format ( output_format ) > Test-2\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/var/lib/jenkins/jobs/G-framework/workspace/test/functional/test_toolbox.py\", line 289, in test_tool\r\n    self.do_it( td )\r\n  File \"/var/lib/jenkins/jobs/G-framework/workspace/test/functional/test_toolbox.py\", line 73, in do_it\r\n    raise e\r\nJobOutputsError: Dataset metadata verification for [file_ext] failed, expected [fastqillumina] but found [txt].\r\n```"},"comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments/141231270","html_url":"https://github.com/galaxyproject/galaxy/issues/744#issuecomment-141231270","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/744","id":141231270,"user":{"login":"martenson","id":1814954,"avatar_url":"https://avatars.githubusercontent.com/u/1814954?v=3","gravatar_id":"","url":"https://api.github.com/users/martenson","html_url":"https://github.com/martenson","followers_url":"https://api.github.com/users/martenson/followers","following_url":"https://api.github.com/users/martenson/following{/other_user}","gists_url":"https://api.github.com/users/martenson/gists{/gist_id}","starred_url":"https://api.github.com/users/martenson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/martenson/subscriptions","organizations_url":"https://api.github.com/users/martenson/orgs","repos_url":"https://api.github.com/users/martenson/repos","events_url":"https://api.github.com/users/martenson/events{/privacy}","received_events_url":"https://api.github.com/users/martenson/received_events","type":"User","site_admin":false},"created_at":"2015-09-17T21:20:20Z","updated_at":"2015-09-17T21:20:20Z","body":"installed samtools on n2, now 3 tests are failing, the above two and\r\n```\r\nFAIL: compare_bam_as_sam ( compare_bam_as_sam ) > Test-1\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/var/lib/jenkins/jobs/G-framework/workspace/test/functional/test_toolbox.py\", line 289, in test_tool\r\n    self.do_it( td )\r\n  File \"/var/lib/jenkins/jobs/G-framework/workspace/test/functional/test_toolbox.py\", line 73, in do_it\r\n    raise e\r\nJobOutputsError: History item  different than expected, difference (using diff):\r\n( /tmp/tmpZtcu66/tmpaSR218/new_files_path_ckRhAB/local_bam_converted_to_sam_SjShwu.sam v. /tmp/tmpZtcu66/tmpaSR218/new_files_path_ckRhAB/history_bam_converted_to_sam_du001X.sam )\r\n--- local_file\r\n+++ history_data\r\n@@ -1,4 +1,4 @@\r\n-@HD\tVN:1.0\tSO:unsorted\r\n+@HD\tVN:1.0\tSO:coordinate\r\n @SQ\tSN:chr10\tLN:135374737\r\n @SQ\tSN:chr10_random\tLN:113275\r\n @SQ\tSN:chr11\tLN:134452384\r\n@@ -62,12 +62,12 @@\r\n @SQ\tSN:chr15_random\tLN:784346\r\n @SQ\tSN:chr16\tLN:88827254\r\n HWI-EAS91_1_30788AAXX:1:1:1095:605\t0\tchrM\t23\t25\t36M\t*\t0\t0\tAAGCAAGNNACTGAAAATGCCTAGATGAGTATTCTT\tIIIIIII\"\"IIIIIIIIIIIIIIIEIIIIIIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n+HWI-EAS91_1_30788AAXX:1:1:606:460\t0\tchrM\t4552\t25\t36M\t*\t0\t0\tTTAATTTNNATTATAATAACACTCACAATATTCATA\tIIIIIII\"\"IIIIIIIIIIIIIIIIII?I6IIIII6\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n+HWI-EAS91_1_30788AAXX:1:1:1082:719\t16\tchrM\t7191\t25\t36M\t*\t0\t0\tTAAATTAACCCATACCAGCACCATAGANNCTCAAGA\t<III0EII3+3I29I>III8AIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n+HWI-EAS91_1_30788AAXX:1:1:1059:362\t16\tchrM\t7348\t25\t36M\t*\t0\t0\tGGCCACCAATGATACTGAAGCTACGAGNNTACCGAT\tII/<)2IIIIIIIIIIIIIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n+HWI-EAS91_1_30788AAXX:1:1:799:192\t16\tchrM\t8421\t25\t36M\t*\t0\t0\tCCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT\tII%::I<IIIIIEIII8IIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n+HWI-EAS91_1_30788AAXX:1:1:1746:1180\t16\tchrM\t12013\t25\t36M\t*\t0\t0\tCCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT\tIIIIIIIIFIIIIIIIIIIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n+HWI-EAS91_1_30788AAXX:1:1:1273:600\t16\tchrM\t13855\t25\t36M\t*\t0\t0\tGTATTAGACACCCATACCTCAGGATACNNCTCAGTA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n HWI-EAS91_1_30788AAXX:1:1:1650:1185\t0\tchrM\t14956\t25\t36M\t*\t0\t0\tACCCCAGNNAACCCTCTCAGCACTCCCCCTCATATT\tIIIIIII\"\"IIIIIIIIIIII6IIIIIIIII5I-II\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n-HWI-EAS91_1_30788AAXX:1:1:799:192\t16\tchrM\t8421\t25\t36M\t*\t0\t0\tCCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT\tII%::I<IIIIIEIII8IIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n-HWI-EAS91_1_30788AAXX:1:1:1082:719\t16\tchrM\t7191\t25\t36M\t*\t0\t0\tTAAATTAACCCATACCAGCACCATAGANNCTCAAGA\t<III0EII3+3I29I>III8AIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n-HWI-EAS91_1_30788AAXX:1:1:1746:1180\t16\tchrM\t12013\t25\t36M\t*\t0\t0\tCCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT\tIIIIIIIIFIIIIIIIIIIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n-HWI-EAS91_1_30788AAXX:1:1:606:460\t0\tchrM\t4552\t25\t36M\t*\t0\t0\tTTAATTTNNATTATAATAACACTCACAATATTCATA\tIIIIIII\"\"IIIIIIIIIIIIIIIIII?I6IIIII6\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n-HWI-EAS91_1_30788AAXX:1:1:1059:362\t16\tchrM\t7348\t25\t36M\t*\t0\t0\tGGCCACCAATGATACTGAAGCTACGAGNNTACCGAT\tII/<)2IIIIIIIIIIIIIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n HWI-EAS91_1_30788AAXX:1:1:1483:1161\t16\tchrM\t15080\t25\t36M\t*\t0\t0\tTCCTGATCCTAGCACTCATCCCCACCCNNCACATAT\tHIIIIIFIIAIHIIIIIIIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n-HWI-EAS91_1_30788AAXX:1:1:1273:600\t16\tchrM\t13855\t25\t36M\t*\t0\t0\tGTATTAGACACCCATACCTCAGGATACNNCTCAGTA\tIIIIIIIIIIIIIIIIIIIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n HWI-EAS91_1_30788AAXX:1:1:1190:1283\t16\tchrM\t15338\t25\t36M\t*\t0\t0\tTATATCGCACATTACCCTGGTCTTGTANNCCAGAAA\tEIII?-IIIIIAIIIIIIIIIIIIIII\"\"IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\r\n```"}}