{"action":"created","issue":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3997","repository_url":"https://api.github.com/repos/Homebrew/homebrew-science","labels_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3997/labels{/name}","comments_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3997/comments","events_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3997/events","html_url":"https://github.com/Homebrew/homebrew-science/pull/3997","id":169042963,"number":3997,"title":"trans-abyss 1.5.5","user":{"login":"ilovezfs","id":5268928,"avatar_url":"https://avatars.githubusercontent.com/u/5268928?v=3","gravatar_id":"","url":"https://api.github.com/users/ilovezfs","html_url":"https://github.com/ilovezfs","followers_url":"https://api.github.com/users/ilovezfs/followers","following_url":"https://api.github.com/users/ilovezfs/following{/other_user}","gists_url":"https://api.github.com/users/ilovezfs/gists{/gist_id}","starred_url":"https://api.github.com/users/ilovezfs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ilovezfs/subscriptions","organizations_url":"https://api.github.com/users/ilovezfs/orgs","repos_url":"https://api.github.com/users/ilovezfs/repos","events_url":"https://api.github.com/users/ilovezfs/events{/privacy}","received_events_url":"https://api.github.com/users/ilovezfs/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Homebrew/homebrew-science/labels/New%20version","name":"New version","color":"009800"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-08-03T04:02:40Z","updated_at":"2016-09-09T21:11:50Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/pulls/3997","html_url":"https://github.com/Homebrew/homebrew-science/pull/3997","diff_url":"https://github.com/Homebrew/homebrew-science/pull/3997.diff","patch_url":"https://github.com/Homebrew/homebrew-science/pull/3997.patch"},"body":"Created with `brew bump-formula-pr`."},"comment":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/comments/246041191","html_url":"https://github.com/Homebrew/homebrew-science/pull/3997#issuecomment-246041191","issue_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3997","id":246041191,"user":{"login":"jonchang","id":213484,"avatar_url":"https://avatars.githubusercontent.com/u/213484?v=3","gravatar_id":"","url":"https://api.github.com/users/jonchang","html_url":"https://github.com/jonchang","followers_url":"https://api.github.com/users/jonchang/followers","following_url":"https://api.github.com/users/jonchang/following{/other_user}","gists_url":"https://api.github.com/users/jonchang/gists{/gist_id}","starred_url":"https://api.github.com/users/jonchang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jonchang/subscriptions","organizations_url":"https://api.github.com/users/jonchang/orgs","repos_url":"https://api.github.com/users/jonchang/repos","events_url":"https://api.github.com/users/jonchang/events{/privacy}","received_events_url":"https://api.github.com/users/jonchang/received_events","type":"User","site_admin":false},"created_at":"2016-09-09T21:11:50Z","updated_at":"2016-09-09T21:11:50Z","body":"```\r\n $ brew test -v trans-abyss\r\nTesting homebrew/science/trans-abyss\r\n==> Using the sandbox\r\n/usr/bin/sandbox-exec -f /tmp/homebrew20160909-71181-1m9hrxw.sb /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -W0 -I /usr/local/Library/Homebrew -- /usr/local/Library/Homebrew/test.rb /usr/local/Library/Taps/homebrew/homebrew-science/trans-abyss.rb -v\r\n==> /usr/local/Cellar/trans-abyss/1.5.5/bin/transabyss --help\r\nusage: transabyss [-h] [--version] [--se PATH [PATH ...]]\r\n                  [--pe PATH [PATH ...]] [--SS] [--outdir PATH] [--name STR]\r\n                  [--stage {dbg,unitigs,contigs,references,junctions,final}]\r\n                  [--length INT] [--cleanup {0,1,2,3}] [--threads INT]\r\n                  [--mpi INT] [-k INT] [-c INT] [-e INT] [-E INT] [-q INT]\r\n                  [-Q INT] [-n INT] [-s INT] [--gsim INT] [--indel INT]\r\n                  [--island INT] [--useblat] [--pid FLOAT] [--walk FLOAT]\r\n                  [--noref]\r\n\r\nAssemble RNAseq with Trans-ABySS.\r\n\r\noptional arguments:\r\n  -h, --help            show this help message and exit\r\n  --version             show program's version number and exit\r\n\r\nInput:\r\n  --se PATH [PATH ...]  single-end read files\r\n  --pe PATH [PATH ...]  paired-end read files\r\n  --SS                  input reads are strand-specific\r\n\r\nBasic Options:\r\n  --outdir PATH         output directory [/private/tmp/trans-abyss-\r\n                        test-20160909-71182-1u4ecma/transabyss_1.5.5_assembly]\r\n  --name STR            assembly name [transabyss] (ie. output assembly:\r\n                        'transabyss-final.fa')\r\n  --stage {dbg,unitigs,contigs,references,junctions,final}\r\n                        run up to the specified stage [final]\r\n  --length INT          minimum output sequence length [100]\r\n  --cleanup {0,1,2,3}   level of clean-up of intermediate files [1]\r\n\r\nABySS Parameters:\r\n  --threads INT         number of threads ('j' in abyss-pe) [1]\r\n  --mpi INT             number of MPI processes ('np' in abyss-pe) [0]\r\n  -k INT, --kmer INT    k-mer size [32]\r\n  -c INT, --cov INT     minimum mean k-mer coverage of a unitig [2]\r\n  -e INT, --eros INT    minimum erosion k-mer coverage [c]\r\n  -E INT, --seros INT   minimum erosion k-mer coverage per strand [0]\r\n  -q INT, --qends INT   minimum base quality on 5' and 3' ends of a read [3]\r\n  -Q INT, --qall INT    minimum base quality throughout a read\r\n  -n INT, --pairs INT   minimum number of pairs for building contigs [2]\r\n  -s INT, --seed INT    minimum unitig size for building contigs [k]\r\n\r\nAdvanced Options:\r\n  --gsim INT            maximum iterations of graph simplification [2]\r\n  --indel INT           indel size tolerance [1]\r\n  --island INT          minimum length of island unitigs [0]\r\n  --useblat             use BLAT alignments to remove redundant sequences.\r\n  --pid FLOAT           minimum percent sequence identity of redundant\r\n                        sequences [0.95]\r\n  --walk FLOAT          percentage of mean k-mer coverage of seed for path-\r\n                        walking [0.05]\r\n  --noref               do not include reference paths in final assembly\r\n\r\nWritten by Ka Ming Nip.\r\nCopyright 2016 Canada's Michael Smith Genome Sciences Centre\r\nReport bugs to <trans-abyss@googlegroups.com>\r\n==> /usr/local/Cellar/trans-abyss/1.5.5/bin/transabyss-analyze --help\r\nFailed to execute: /usr/local/Cellar/trans-abyss/1.5.5/bin/transabyss-analyze\r\n==> Sandbox log\r\nSep  9 14:11:27 kernel[0]: Sandbox: Python(71192) deny(1) file-write-create /usr/local/Cellar/trans-abyss/1.5.5/utilities/fasta_utils.pyc\r\nSep  9 14:11:27 kernel[0]: Sandbox: Python(71192) deny(1) file-write-create /usr/local/Cellar/trans-abyss/1.5.5/utilities/sam_cid_extractor.pyc\r\nError: homebrew/science/trans-abyss: failed\r\nFailed executing: /usr/local/Cellar/trans-abyss/1.5.5/bin/transabyss-analyze --help\r\n/usr/local/Library/Homebrew/formula.rb:1608:in `block in system'\r\n/usr/local/Library/Homebrew/formula.rb:1545:in `open'\r\n/usr/local/Library/Homebrew/formula.rb:1545:in `system'\r\n/usr/local/Library/Taps/homebrew/homebrew-science/trans-abyss.rb:33:in `block in <class:TransAbyss>'\r\n/usr/local/Library/Homebrew/formula.rb:1446:in `block (2 levels) in run_test'\r\n/usr/local/Library/Homebrew/formula.rb:775:in `with_logging'\r\n/usr/local/Library/Homebrew/formula.rb:1445:in `block in run_test'\r\n/usr/local/Library/Homebrew/extend/fileutils.rb:14:in `block in mktemp'\r\n/usr/local/Library/Homebrew/extend/fileutils.rb:74:in `block in run'\r\n/usr/local/Library/Homebrew/extend/fileutils.rb:74:in `chdir'\r\n/usr/local/Library/Homebrew/extend/fileutils.rb:74:in `run'\r\n/usr/local/Library/Homebrew/extend/fileutils.rb:13:in `mktemp'\r\n/usr/local/Library/Homebrew/formula.rb:1439:in `run_test'\r\n/usr/local/Library/Homebrew/test.rb:28:in `block in <main>'\r\n/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/timeout.rb:66:in `timeout'\r\n/usr/local/Library/Homebrew/test.rb:27:in `<main>'\r\n```"}}
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