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Error when following the example biobox usage #218

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andre-geldenhuis opened this issue Jun 27, 2018 · 0 comments
Open

Error when following the example biobox usage #218

andre-geldenhuis opened this issue Jun 27, 2018 · 0 comments

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@andre-geldenhuis
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When following the example velvet biobox usage on bioboxes.org - bioboxes throws and error

...
    with open(os.path.join(dir_, 'biobox.yaml'), 'r') as f:
IOError: [Errno 2] No such file or directory: '/tmp/tmprgcdRz/biobox.yaml'

This is running in a fresh ubuntu VM (ubuntu 18.04) with 4 core and 8 gigs of ram.

For reference the example usage is

# Fetch the velvet assembler image using Docker
docker pull bioboxes/velvet

# Use the velvet biobox to assemble these reads
biobox run \
  short_read_assembler \
  bioboxes/velvet \
  --input reads.fq.gz \
  --output contigs.fa

The fasta file reads.fq.gz is in the same directory.

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