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I tried using Bioboxes for the first time using the demo commands. It ran for about 45 seconds before erroring with the trace below:
$ pip2 install --user biobox_cli
[ lots of output, ran successfully ]
$ /home/jorvis/.local/bin/biobox run short_read_assembler bioboxes/megahit --input SRS015996.denovo_duplicates_marked.trimmed.1.fastq --output megahit_test_dir1only
Traceback (most recent call last):
File "/home/jorvis/.local/bin/biobox", line 9, in <module>
biobox.run()
File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/main.py", line 30, in run
util.select_module("command", opts["<command>"]).run(args)
File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/command/run.py", line 26, in run
ctnr = bbx.run(argv)
File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/biobox_helper.py", line 42, in run
self.after_run(output, output_dir)
File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/biobox_type/short_read_assembler.py", line 36, in after_run
biobox_output = fle.get_biobox_file_contents(host_dst_dir)
File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/biobox_file.py", line 9, in get_biobox_file_contents
with open(os.path.join(dir_, 'biobox.yaml'), 'r') as f:
IOError: [Errno 2] No such file or directory: '/tmp/tmpbSgC_Y/biobox.yaml'
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