Mercurial > repos > dereeper > sniploid2
comparison SNiPloid.sh @ 0:e94de0ea3351 draft default tip
Uploaded
| author | dereeper |
|---|---|
| date | Wed, 11 Sep 2013 09:08:15 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:e94de0ea3351 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 | |
| 4 directory=`dirname $0` | |
| 5 | |
| 6 if [ -d "$HOME/galaxy_dist/static/images" ]; then | |
| 7 cp -rf $directory/img_sniploid $HOME/galaxy_dist/static/images | |
| 8 fi | |
| 9 if [ -d "$HOME/galaxy-dist/static/images" ]; then | |
| 10 cp -rf $directory/img_sniploid $HOME/galaxy-dist/static/images | |
| 11 fi | |
| 12 | |
| 13 | |
| 14 if [ "$1" = "poly" ] # poly analysis | |
| 15 then | |
| 16 perl $directory/SNiPloid.pl --dp $2 --dp2 $3 --vp $4 --cpp $5 --vp2 $6 --cpp2 $7 --oc $8 --oh $9 --ohs ${10} --ocs ${11} --elq ${12} --vfp1 ${14} --vfp2 ${15} --img ../../../static/images/img_sniploid/ 2>&1 >>${13} | |
| 17 if [ "${16}" = "yes" ] | |
| 18 then | |
| 19 perl $directory/DrawMapOfOccurences.pl -c ${11} -a ${17} -o ${18} -m 50 -t polyploid_polyploid | |
| 20 fi | |
| 21 elif [ $2 -eq 0 ] # Ref ext | |
| 22 then | |
| 23 perl $directory/SNiPloid.pl --dp $3 --dg1 $4 --vp $5 --cpp $6 --vg1 $7 --cg1 $8 --dg2 $9 --vg2 $10 --cg2 $11 -- ref 0 --oc ${12} --oh ${13} --ohs ${14} --ocs ${15} --elq ${16} --img ../../../static/images/img_sniploid/ 2>&1 >>${17} | |
| 24 else # Ref int == 1 | |
| 25 perl $directory/SNiPloid.pl --gn2 $3 --dp $4 --dg1 $5 --vp $6 --cpp $7 --vg1 $8 --cg1 $9 --ref 1 --oc ${10} --oh ${11} --ohs ${12} --ocs ${13} --elq ${14} --img ../../../static/images/img_sniploid/ 2>&1 >>${15} | |
| 26 if [ "${16}" = "yes" ] | |
| 27 then | |
| 28 echo ${16} >>${15} | |
| 29 perl $directory/DrawMapOfOccurences.pl -c ${13} -a ${17} -o ${18} -m 50 -t polyploid_diploid 2>&1 >>${15} | |
| 30 fi | |
| 31 fi |