47 lines
1.1 KiB
Bash
47 lines
1.1 KiB
Bash
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#!/bin/sh
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#
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# Downloads the sequence for a strain of e. coli from NCBI and builds a
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# Bowtie index for it
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#
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GENOMES_MIRROR=ftp://ftp.ncbi.nlm.nih.gov/genomes
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BOWTIE_BUILD_EXE=./bowtie2-build
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if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
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if ! which bowtie2-build ; then
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echo "Could not find bowtie2-build in current directory or in PATH"
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exit 1
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else
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BOWTIE_BUILD_EXE=`which bowtie2-build`
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fi
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fi
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if [ ! -f NC_008253.fna ] ; then
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if ! which wget > /dev/null ; then
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echo wget not found, looking for curl...
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if ! which curl > /dev/null ; then
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echo curl not found either, aborting...
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else
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# Use curl
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curl ${GENOMES_MIRROR}/Bacteria/Escherichia_coli_536_uid58531/NC_008253.fna -o NC_008253.fna
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fi
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else
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# Use wget
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wget ${GENOMES_MIRROR}/Bacteria/Escherichia_coli_536_uid58531/NC_008253.fna
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fi
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fi
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if [ ! -f NC_008253.fna ] ; then
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echo "Could not find NC_008253.fna file!"
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exit 2
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fi
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CMD="${BOWTIE_BUILD_EXE} $* -t 8 NC_008253.fna e_coli"
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echo $CMD
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if $CMD ; then
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echo "e_coli index built; you may remove fasta files"
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else
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echo "Index building failed; see error message"
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fi
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