Lines Matching refs:wrkdir

10 $wrkdir        = shift;
27 if (! -e $wrkdir)        { die "$wrkdir doesn't exist"; }
38 …$cmd  = "esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname";                                   …
39 …$cmd  = "esl-seqstat --amino -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'";            …
43 …$cmd = "esl-sfetch -o $wrkdir/$msaname.query $wrkdir/$msaname.sto $qname > /dev/null";            …
45 …$cmd = "$jackhmmer $iteropts -A $wrkdir/$msaname.jck $wrkdir/$msaname.query $fafile.iter > /dev/nu…
46 …$cmd = "$hmmbuild --hand $wrkdir/$msaname.hmm $wrkdir/$msaname.jck > /dev/null`";                 …
47 …$cmd = "$hmmsearch $searchopts --tblout $wrkdir/$msaname.tmp $wrkdir/$msaname.hmm $fafile > /dev/n…
49 …if (! open(OUTPUT, "$wrkdir/$msaname.tmp")) { print "FAILED: to open $wrkdir/$msaname.tmp"; next M…
60     unlink "$wrkdir/$msaname.tmp";
61     unlink "$wrkdir/$msaname.hmm";
62     unlink "$wrkdir/$msaname.jck";
63     unlink "$wrkdir/$msaname.query";
64     unlink "$wrkdir/$msaname.sto";