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Batch or not if/then
10-23-2014
10-23-2014
10-23-2014
#!/bin/sh
...
perl -e 'exec("exec perl ...");'
...
10-24-2014
while read id
do
/home/cmccabe/test.sh: line 6: syntax error near unexpected token `done' /home/cmccabe/test.sh: line 6: ` done'
while read id
do
. #!/bin/bash
while true
do
printf "Is this a batch :"
while read id
done
do
case "$id" in
[yY]) perl -e 'exec("exec perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt");'
;;
[nN]) # code for X
printf "Enter ID : " ; read id
[ -z "$id" ] && break
[ "$id" = "end" ] && break
perl -e 'exec("exec perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo");'
;;
end) break ;;
*) ;; # Unknown option, do nothing
esac
printf "Is this a batch :"
done
10-24-2014
#!/bin/bash
while true
do
printf "Is this a batch :"
case "$id" in
[yY]) echo "perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt
;;
[nN]) # code for X
printf "Enter ID : " ; read id
[ -z "$id" ] && break
[ "$id" = "end" ] && break
echo ("perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo
;;
end) break ;;
*) ;; # Unknown option, do nothing
esac
printf "Is this a batch :"
done.|
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