{"action":"created","issue":{"url":"https://api.github.com/repos/bioboxes/rfc/issues/187","repository_url":"https://api.github.com/repos/bioboxes/rfc","labels_url":"https://api.github.com/repos/bioboxes/rfc/issues/187/labels{/name}","comments_url":"https://api.github.com/repos/bioboxes/rfc/issues/187/comments","events_url":"https://api.github.com/repos/bioboxes/rfc/issues/187/events","html_url":"https://github.com/bioboxes/rfc/issues/187","id":115777356,"number":187,"title":"Suggested changes to the assembly validator output interface","user":{"login":"michaelbarton","id":1142,"avatar_url":"https://avatars.githubusercontent.com/u/1142?v=3","gravatar_id":"","url":"https://api.github.com/users/michaelbarton","html_url":"https://github.com/michaelbarton","followers_url":"https://api.github.com/users/michaelbarton/followers","following_url":"https://api.github.com/users/michaelbarton/following{/other_user}","gists_url":"https://api.github.com/users/michaelbarton/gists{/gist_id}","starred_url":"https://api.github.com/users/michaelbarton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/michaelbarton/subscriptions","organizations_url":"https://api.github.com/users/michaelbarton/orgs","repos_url":"https://api.github.com/users/michaelbarton/repos","events_url":"https://api.github.com/users/michaelbarton/events{/privacy}","received_events_url":"https://api.github.com/users/michaelbarton/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2015-11-09T01:42:48Z","updated_at":"2017-02-17T16:41:07Z","closed_at":"2017-02-17T16:41:07Z","body":"In relation to #184, I was testing the assembly benchmarking interface with\nquast. I initially ran:\n\n```\nbiobox\n  run \\\n  assembler_benchmark \\\n  bioboxes/quast \\\n  --input-fasta=contigs.fa \\\n  --output=output\n```\n\nThis however failed because the argument `--input-ref` is required. I don't\nhave a reference genome for my contigs, however a directory is still required\neven if it is empty. I next ran the command:\n\n```\nbiobox\n  run \\\n  assembler_benchmark \\\n  bioboxes/quast \\\n  --input-fasta=contigs.fa \\\n  --input-ref=ref \\\n  --output=metrics.txt\n```\n\nThis produced the following error:\n\n```\nTraceback (most recent call last):\n  File \"/Users/michaelbarton/Library/Python/2.7/bin/biobox\", line 9, in <module>\n    biobox.run()\n  File \"/Users/michaelbarton/Library/Python/2.7/lib/python/site-packages/biobox_cli/main.py\", line 30, in run\n    util.select_module(\"command\", opts[\"<command>\"]).run(args)\n  File \"/Users/michaelbarton/Library/Python/2.7/lib/python/site-packages/biobox_cli/command/run.py\", line 24, in run\n    ctnr = bbx.run(argv)\n  File \"/Users/michaelbarton/Library/Python/2.7/lib/python/site-packages/biobox_cli/biobox.py\", line 29, in run\n    self.after_run(output, host_dst_dir)\n  File \"/Users/michaelbarton/Library/Python/2.7/lib/python/site-packages/biobox_cli/biobox_type/assembler_benchmark.py\", line 52, in after_run\n    self.copy_result_files(host_dst_dir, output)\n  File \"/Users/michaelbarton/Library/Python/2.7/lib/python/site-packages/biobox_cli/biobox_type/assembler_benchmark.py\", line 26, in copy_result_files\n    map(lambda f: shutil.move(os.path.join(biobox_output_dir,f), dst), output_files)\n  File \"/Users/michaelbarton/Library/Python/2.7/lib/python/site-packages/biobox_cli/biobox_type/assembler_benchmark.py\", line 26, in <lambda>\n    map(lambda f: shutil.move(os.path.join(biobox_output_dir,f), dst), output_files)\n  File \"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py\", line 299, in move\n    copytree(src, real_dst, symlinks=True)\n  File \"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py\", line 177, in copytree\n    os.makedirs(dst)\n  File \"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.py\", line 157, in makedirs\n    mkdir(name, mode)\nOSError: [Errno 17] File exists: 'metrics'\n```\n\nTrying the same command with different output names produces the same error\nwith the corresponding name. Each time this created a file with the output\nname. The command works correctly if the the output directly is created first\nbefore running. When I run the command again the file `output/biobox.yaml` is\ncreated with the contents:\n\n``` yaml\nversion: 0.9.0\nresults:\n  - name: HTML\n    type: html\n    inline: false\n    value: combined_quast_output/standalone_report.html\n    description: A summary of multiple metrics.\n```\n\nA text file with the QUAST metics for the assemly are in the file\n`output/combined_quast_output/report.tsv`.\n## Suggested changes\n- The directory with reference genomes is optional. If this directory is not\n  an argument, then the non-reference assembly metrics should be returned. I\n  believe this follows the assembler benchmark signature where the fastq\n  directory is optional.\n- In the command line interface I think the `--output` flag should create a\n  yaml file containing metrics of the benchmark evaluation instead of a\n  directory with the quast generated files. I suggest this because the CLI is\n  a simplied subset of using bioboxes for the most common cases. For example\n  this is the case in the short_read_assembler CLI. This would also be a\n  consistent UX when there are assembler benchmarks other than quast.\n\nWhat do you think?\n"},"comment":{"url":"https://api.github.com/repos/bioboxes/rfc/issues/comments/280700894","html_url":"https://github.com/bioboxes/rfc/issues/187#issuecomment-280700894","issue_url":"https://api.github.com/repos/bioboxes/rfc/issues/187","id":280700894,"user":{"login":"michaelbarton","id":1142,"avatar_url":"https://avatars.githubusercontent.com/u/1142?v=3","gravatar_id":"","url":"https://api.github.com/users/michaelbarton","html_url":"https://github.com/michaelbarton","followers_url":"https://api.github.com/users/michaelbarton/followers","following_url":"https://api.github.com/users/michaelbarton/following{/other_user}","gists_url":"https://api.github.com/users/michaelbarton/gists{/gist_id}","starred_url":"https://api.github.com/users/michaelbarton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/michaelbarton/subscriptions","organizations_url":"https://api.github.com/users/michaelbarton/orgs","repos_url":"https://api.github.com/users/michaelbarton/repos","events_url":"https://api.github.com/users/michaelbarton/events{/privacy}","received_events_url":"https://api.github.com/users/michaelbarton/received_events","type":"User","site_admin":false},"created_at":"2017-02-17T16:41:07Z","updated_at":"2017-02-17T16:41:07Z","body":"The assembly metrics output will be implemented in bioboxes/rfc#204. I will close this issue in favor of that one."}}
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