annotate genes with prokka #20
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boris-dimitrov
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boris-dimitrov
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Dec 17, 2019
| # bioinformatics | ||
| RUN apt-get install -y samtools bowtie2 vsearch | ||
| RUN pip3 install pysam biopython |
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pysam no longer build successfully
fortunately it is not yet needed
we hope in future it gets fixed
boris-dimitrov
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Dec 17, 2019
| @@ -35,18 +31,32 @@ RUN apt-get remove -y ncbi-blast+ | |||
| RUN wget -N ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-1.x86_64.rpm | |||
| RUN alien -i ncbi-blast-2.9.0+-1.x86_64.rpm | |||
| RUN rm -rf ncbi-blast-2.9.0+-1.x86_64.rpm | |||
| RUN bash -c "yes | cpan Bio::Perl" | |||
| # The following line differs from the official instructions in that it actually works. | |||
| RUN cpan List::Util | |||
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Thank you internet.
boris-dimitrov
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Dec 17, 2019
| # mv linux.tbl2asn tbl2asn && \ | ||
| # chmod +x tbl2asn && \ | ||
| # mv tbl2asn /usr/local/prokka/binaries/linux/ | ||
|
|
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For now we are sticking with prokka but in future we would consider using just prodigal because of this dependency --- which means in a few months this docker build will need to be repeated, with all corresponding fragility.
boris-dimitrov
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Dec 17, 2019
| try: | ||
| command(f"set -o pipefail; lz4 -c {src} | aws s3 cp --only-show-errors - {dst}", check=check) | ||
| except: | ||
| command(f"aws s3 rm {dst}", check=False) |
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If src doesn't exist, the above command would create an empty destination. Work around that. Perhaps we should also just check that src exists.
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As documented in https://github.com/czbiohub/iggtools/wiki#gene-annotations