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biobricks-ai / uniprot

UniProt is a freely accessible database of protein sequence and functional information
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dvc repro fails #2

Open tomlue opened 2 years ago

tomlue commented 2 years ago

dvc repro fails with error

bash/convert: line 23: 27742 Broken pipe             gunzip -c $input_file
     27743                       | sed '1,4d'
     27744                       | sed '1s/^/<uniprot>\n/'
     27745                       | sed 's/xmlns.*=".*"//g'
     27746 Killed                  | xsltproc -o $output_file $xsl_file -
ERROR: failed to reproduce 'process': failed to run: bash/convert download/uniprot_sprot.xml.gz xsl/uniprot.xsl data/uniprot_sprot.csv, exited with 137
jborden commented 2 years ago

is this being run in the docker container?

tomlue commented 2 years ago

No

On Tue, May 24, 2022 at 4:27 PM James Borden @.***> wrote:

is this being run in the docker container?

— Reply to this email directly, view it on GitHub https://github.com/biobricks-ai/uniprot/issues/2#issuecomment-1136399328, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAPFFTRNNDYW2NF3OEMWJGTVLU3UJANCNFSM5W2YYN7A . You are receiving this because you authored the thread.Message ID: @.***>

jborden commented 2 years ago

not sure what environment you are in, it runs fine for me with a freshly cloned repo on ws2. you need xsltproc in order to make this work, the R xml2 parser wasn't up to the task and had out-of-memory crashes

tomlue commented 2 years ago

ok, we'll need to add dependency steps to bricks and checks to bricktools soon.