/usr/share/doc/ssake/examples/runSSAKE.sh is in ssake-examples 3.8.4-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 | #!/bin/sh
#!/usr/bin/bash
# USAGE: ./runSSAKE.sh <read1.fq> <read2.fq> <library fragment length(bp)> <basename>
d=`date`
if [ "$1" == "" ] || [ "$2" == "" ] || [ "$3" == "" ] || [ "$4" == "" ]; then
echo USAGE: ./runSSAKE.sh read1.fq read2.fq libFragLength basename
exit
fi
echo Running: ./runSSAKE.sh $1 $2 $3 $4
echo ===================================================================================
echo $d : Running SSAKE assembly pipeline on reads file:
echo $1
echo $2
echo target fragment length = $3 bp
echo basename for assembly : $4
d=`date`
echo -----------------------------------------------------------------------------------
echo $d : Trimming low quality bases, be patient...
echo -----------------------------------------------------------------------------------
echo $1 > filesToTrim.fof
echo $2 >> filesToTrim.fof
/home/rwarren/SSAKE_dev/ssake_v3.8.4/tools/TQSfastq.pl -f filesToTrim.fof -q 20 -n 70 -e 33
cat $1c70q20e33.fa |perl -ne 'if(/^(\>\@\S+)/){print "$1b\n";}else{print;}' > read1.trimmed.fa
cat $2c70q20e33.fa |perl -ne 'if(/^(\>\@\S+)/){print "$1a\n";}else{print;}' > read2.trimmed.fa
d=`date`
echo -----------------------------------------------------------------------------------
echo $d : Formatting fasta input for SSAKE...
echo -----------------------------------------------------------------------------------
/home/rwarren/SSAKE_dev/ssake_v3.8.4/tools/makePairedOutput2UNEQUALfiles.pl read1.trimmed.fa read2.trimmed.fa $3
d=`date`
echo -----------------------------------------------------------------------------------
echo $d : Initiating SSAKE...
echo -----------------------------------------------------------------------------------
/usr/bin/time -v -o $4.time /home/rwarren/SSAKE_dev/ssake_v3.8.4/SSAKE -f paired.fa -p 1 -g unpaired.fa -m 20 -w 5 -b $4
d=`date`
echo -----------------------------------------------------------------------------------
echo $d : Converting scaffold .csv into fasta file...
echo -----------------------------------------------------------------------------------
/home/rwarren/SSAKE_dev/ssake_v3.8.4/tools/makeFastaFileFromScaffolds.pl $4.scaffolds
d=`date`
echo -----------------------------------------------------------------------------------
echo $d : Computing stats
echo -----------------------------------------------------------------------------------
/home/rwarren/SSAKE_dev/ssake_v3.8.4/tools/getStats.pl $4.contigs > $4.contigs.stats
d=`date`
echo -----------------------------------------------------------------------------------
echo $d : Computing stats from $4.scaffolds.fa
echo -----------------------------------------------------------------------------------
/home/rwarren/SSAKE_dev/ssake_v3.8.4/tools/getStats.pl $4.scaffolds.fa > $4.scaffolds.stats
d=`date`
echo -----------------------------------------------------------------------------------
echo $d : assembly pipeline complete. Results are under $4.
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