/usr/share/doc/ssake/examples/MiSeqCampylobacterAssembly.sh is in ssake-examples 3.8.2-1.
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 | d=`date`
echo -----------------------------------------------------------------------------------
echo Running SSAKE assembly pipeline on bacterial sequence data. It will need ca.4GB RAM
echo ------------------------------------------------------------------------------------
echo Downloading trimmed/formatted data for Campylobacter showae on $d ...
echo ------------------------------------------------------------------------------------
wget ftp://ftp.bcgsc.ca/supplementary/SSAKE/CC57C*
echo ------------------------------------------------------------------------------------
echo done. Initiating SSAKE assembly ETA 10-20min depending on system...
echo ------------------------------------------------------------------------------------
time ../SSAKE -f CC57C_paired.fa -p 1 -g CC57C_unpaired.fa -m 20 -w 5 -b CC57C
echo ------------------------------------------------------------------------------------
echo done. Converting scaffold .csv into fasta file...
echo ------------------------------------------------------------------------------------
../tools/makeFastaFileFromScaffolds.pl CC57C.scaffolds
echo ------------------------------------------------------------------------------------
echo done. Computing stats from CC57C.contigs
echo ------------------------------------------------------------------------------------
../tools/getStats.pl CC57C.contigs > CC57C.contigs.stats
echo ------------------------------------------------------------------------------------
echo done. Computing stats from CC57C.scaffolds.fa
echo ------------------------------------------------------------------------------------
../tools/getStats.pl CC57C.scaffolds.fa > CC57C.scaffolds.stats
echo assembly pipeline complete. Results are under CC57C.
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