/usr/share/doc/ssake/examples/MiSeqCampylobacterAssembly.sh is in ssake-examples 4.0-1.
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 | #!/bin/sh
d=`date`
echo -----------------------------------------------------------------------------------
echo Running SSAKE assembly pipeline on bacterial sequence data.
echo ------------------------------------------------------------------------------------
echo Downloading trimmed/formatted data for Campylobacter showae CC57C on $d ...
echo ------------------------------------------------------------------------------------
rm -rf CC57C_paired.fa
rm -rf CC57C_unpaired.fa
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. Computing stats from contigs
echo ------------------------------------------------------------------------------------
../tools/getStats.pl CC57C_contigs.fa 500 > CC57C_contigs_stats.txt
echo ------------------------------------------------------------------------------------
echo done. Computing stats from scaffolds
echo ------------------------------------------------------------------------------------
../tools/getStats.pl CC57C_scaffolds.fa 500 > CC57C_scaffolds_stats.txt
echo assembly pipeline complete. Results are under CC57C.
|