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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
kmer-0~20150903+r2013/libutil/test/endianess.c-11-begin 644 test-alpha
kmer-0~20150903+r2013/libutil/test/endianess.c:12:.`@$$`P(!"`<&!00#`@$`
kmer-0~20150903+r2013/libutil/test/endianess.c-13-`
##############################################
kmer-0~20150903+r2013/libutil/test/endianess.c-15-begin 644 test-i386
kmer-0~20150903+r2013/libutil/test/endianess.c:16:.`@$$`P(!"`<&!00#`@$`
kmer-0~20150903+r2013/libutil/test/endianess.c-17-`
##############################################
kmer-0~20150903+r2013/libutil/test/endianess.c-19-begin 644 test-opteron
kmer-0~20150903+r2013/libutil/test/endianess.c:20:.`@$$`P(!"`<&!00#`@$`
kmer-0~20150903+r2013/libutil/test/endianess.c-21-`
##############################################
kmer-0~20150903+r2013/Make.rules-22- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/Make.rules:23: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/Make.rules:24: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/Make.rules-25- rm -f $$$${Fout} && cp -fp $$$${F} $$$${Fout} ; \
##############################################
kmer-0~20150903+r2013/Make.rules-39- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/Make.rules:40: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/Make.rules:41: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/Make.rules-42- rm -f $$$${Fout}${.EXE} && cp -fp $$$${F}${.EXE} $$$${Fout}${.EXE} ; \
##############################################
kmer-0~20150903+r2013/Make.rules-46- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/Make.rules:47: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/Make.rules:48: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/Make.rules-49- rm -f $$$${Fout} && cp -fp $$$${F} $$$${Fout} ; \
##############################################
kmer-0~20150903+r2013/Make.rules-62- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/Make.rules:63: Fout=$${INSTALL/}$$$${D}`basename $$$${F} .so`${.SO} ; \
kmer-0~20150903+r2013/Make.rules:64: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/Make.rules-65- rm -f $$$${Fout} && cp -fp $$$${F} $$$${Fout} ; \
##############################################
kmer-0~20150903+r2013/Make.rules-78- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/Make.rules:79: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/Make.rules:80: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/Make.rules-81- rm -f $$$${Fout} && cp -fp $$$${F} $$$${Fout} ; \
##############################################
kmer-0~20150903+r2013/Make.rules-106- @ echo "making $@"
kmer-0~20150903+r2013/Make.rules:107: @ dir=`echo $< | sed -e's~[^/]*$$~~'`; \
kmer-0~20150903+r2013/Make.rules-108- ${CCDEP} ${CDEPFLAGS} ${CFLAGS} $< | \
##############################################
kmer-0~20150903+r2013/Make.rules-114- @ echo "making $@"
kmer-0~20150903+r2013/Make.rules:115: @ dir=`echo $< | sed -e's~[^/]*$$~~'`; \
kmer-0~20150903+r2013/Make.rules-116- ${CXXDEP} ${CXXDEPFLAGS} ${CXXFLAGS} $< | \
##############################################
kmer-0~20150903+r2013/Make.rules-218-%.dvi: %.tex
kmer-0~20150903+r2013/Make.rules:219: ${-LATEX} cd `dirname $<` && ${LATEX} `basename $<` && ${LATEX} `basename $<`
kmer-0~20150903+r2013/Make.rules-220-
kmer-0~20150903+r2013/Make.rules-221-%.aux: %.tex
kmer-0~20150903+r2013/Make.rules:222: ${-LATEX} cd `dirname $<` && ${LATEX} `basename $<` && ${LATEX} `basename $<`
kmer-0~20150903+r2013/Make.rules-223-
kmer-0~20150903+r2013/Make.rules-224-%.bbl: %.aux
kmer-0~20150903+r2013/Make.rules:225: ${-LATEX} cd `dirname $<` && ${BIBTEX} `basename ${<:.aux=}`
kmer-0~20150903+r2013/Make.rules-226-
##############################################
kmer-0~20150903+r2013/Make.rules-231-${ALL_TEX_PS}: %.ps: %.dvi
kmer-0~20150903+r2013/Make.rules:232: ${-LATEX} cd `dirname $<` && ${DVIPS} -o `basename $@` `basename $<`
kmer-0~20150903+r2013/Make.rules-233-
kmer-0~20150903+r2013/Make.rules-234-${ALL_TEX_PDF}: %.pdf: %.tex %.aux
kmer-0~20150903+r2013/Make.rules:235: ${-LATEX} cd `dirname $<` && ${PDFLATEX} `basename $<` && ${PDFLATEX} `basename $<`
kmer-0~20150903+r2013/Make.rules-236-__SUBGOALS__+=$${${1:.=.TEX_PS}} $${${1:.=.TEX_PDF}}
##############################################
kmer-0~20150903+r2013/seagen/analysis/plotScoresSingly.pl-43-
kmer-0~20150903+r2013/seagen/analysis/plotScoresSingly.pl:44: system("mkdir $direct") if (! -d "$direct");
kmer-0~20150903+r2013/seagen/analysis/plotScoresSingly.pl-45-
##############################################
kmer-0~20150903+r2013/seagen/analysis/plotScoresSingly.pl-68- $cmd .= " $tmppath/covr-$estid.dat";
kmer-0~20150903+r2013/seagen/analysis/plotScoresSingly.pl:69: system("$cmd");
kmer-0~20150903+r2013/seagen/analysis/plotScoresSingly.pl-70-}
##############################################
kmer-0~20150903+r2013/atac-driver/relabel.pl-19- print STDERR "Dang, gotta grep the deflines!\n";
kmer-0~20150903+r2013/atac-driver/relabel.pl:20: system("grep '>' $file.fasta > $file.deflines");
kmer-0~20150903+r2013/atac-driver/relabel.pl-21- $file = "$file.deflines";
##############################################
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-47-#
kmer-0~20150903+r2013/atac-driver/run-comparison.pl:48:system("mkdir $dir") if (! -d "$dir");
kmer-0~20150903+r2013/atac-driver/run-comparison.pl:49:system("ln -s $amap $dir/amap.atac") if (! -e "$dir/amap.atac");
kmer-0~20150903+r2013/atac-driver/run-comparison.pl:50:system("ln -s $atac $dir/atac.atac") if (! -e "$dir/atac.atac");
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-51-
##############################################
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-54- print STDERR "GAP SHIFTER NEEDS assembly-a, so that the whole genome can be loaded!\n";
kmer-0~20150903+r2013/atac-driver/run-comparison.pl:55: system("$gapShifter -g 1 < $dir/amap.atac > $dir/amap.shift.atac") and die "Failed to shift amap.\n";
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-56-}
##############################################
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-59- print STDERR "GAP SHIFTER NEEDS assembly-a, so that the whole genome can be loaded!\n";
kmer-0~20150903+r2013/atac-driver/run-comparison.pl:60: system("$gapShifter -g 1 < $dir/atac.atac > $dir/atac.shift.atac") and die "Failed to shift atac.\n";
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-61-}
##############################################
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-66-if (! -e "$dir/overlap.map1annotation") {
kmer-0~20150903+r2013/atac-driver/run-comparison.pl:67: system("$overlap $dir/amap.shift.atac $dir/atac.shift.atac $dir/overlap") and die "Failed to overlap.\n";
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-68-}
##############################################
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-85-
kmer-0~20150903+r2013/atac-driver/run-comparison.pl:86: system("$mismatchCounter < $tmp/a.otoi > $tmp/c.otoi") and die "Failed mismatchCounter on A.\n";
kmer-0~20150903+r2013/atac-driver/run-comparison.pl:87: system("$mismatchCounter < $tmp/b.otoi > $tmp/d.otoi") and die "Failed mismatchCounter on B.\n";
kmer-0~20150903+r2013/atac-driver/run-comparison.pl-88- }
##############################################
kmer-0~20150903+r2013/atac-driver/makeplot.pl-199- my $asmAnchorSequence;
kmer-0~20150903+r2013/atac-driver/makeplot.pl:200: my $minAsm = 999999999;
kmer-0~20150903+r2013/atac-driver/makeplot.pl-201-
##############################################
kmer-0~20150903+r2013/atac-driver/makeplot.pl-242- if ($v[9] < $minAsm) {
kmer-0~20150903+r2013/atac-driver/makeplot.pl:243: $minAsm = $v[9];
kmer-0~20150903+r2013/atac-driver/makeplot.pl-244- $refSplit = $v[5];
##############################################
kmer-0~20150903+r2013/atac-driver/makeplot.pl-425-
kmer-0~20150903+r2013/atac-driver/makeplot.pl:426:system("gnuplot $ot.gp");
kmer-0~20150903+r2013/atac-driver/makeplot.pl-427-
##############################################
kmer-0~20150903+r2013/atac-driver/runatac.pl-40-print "$cmd\n";
kmer-0~20150903+r2013/atac-driver/runatac.pl:41:system($cmd) and die "Failed to briatac.pl!\n";
kmer-0~20150903+r2013/atac-driver/runatac.pl-42-
##############################################
kmer-0~20150903+r2013/atac-driver/runatac.pl-47-$cmd .= "/bioinfo/assembly/walenz/src/genomics/atac-driver/clumpMaker/clumpMaker -c 5000 -2 -S -f $name.atac.ckpLast.sorted > $name.atac.ckpLast.clumps";
kmer-0~20150903+r2013/atac-driver/runatac.pl:48:system($cmd) and die "Failed to atacdriver.sh!\n";
kmer-0~20150903+r2013/atac-driver/runatac.pl-49-
##############################################
kmer-0~20150903+r2013/atac-driver/statsGenerator/stats-to-xls.pl-98- } if (m/^TANDEM REPEATS in (.*)$/) {
kmer-0~20150903+r2013/atac-driver/statsGenerator/stats-to-xls.pl:99: my $asm = $1;
kmer-0~20150903+r2013/atac-driver/statsGenerator/stats-to-xls.pl-100-
##############################################
kmer-0~20150903+r2013/atac-driver/alignOverlap/summarizeDisagree.pl-97-
kmer-0~20150903+r2013/atac-driver/alignOverlap/summarizeDisagree.pl:98:system("gnuplot < $outprefix.gnuplot");
kmer-0~20150903+r2013/atac-driver/alignOverlap/summarizeDisagree.pl-99-
##############################################
kmer-0~20150903+r2013/atac-driver/atac.pl-254-
kmer-0~20150903+r2013/atac-driver/atac.pl:255: system("mkdir $ATACdir") if (! -d "$ATACdir");
kmer-0~20150903+r2013/atac-driver/atac.pl:256: system("mkdir $ATACdir/work") if (! -d "$ATACdir/work");
kmer-0~20150903+r2013/atac-driver/atac.pl:257: system("mkdir $ATACdir/stats") if (! -d "$ATACdir/stats");
kmer-0~20150903+r2013/atac-driver/atac.pl:258: system("mkdir $MERYLdir") if (! -d "$MERYLdir");
kmer-0~20150903+r2013/atac-driver/atac.pl-259-}
##############################################
kmer-0~20150903+r2013/atac-driver/atac.pl-321-
kmer-0~20150903+r2013/atac-driver/atac.pl:322: #system("ln -s $seq1 $MERYLdir/$id1.fasta") if (! -e "$MERYLdir/$id1.fasta");
kmer-0~20150903+r2013/atac-driver/atac.pl:323: #system("ln -s $seq2 $MERYLdir/$id2.fasta") if (! -e "$MERYLdir/$id2.fasta");
kmer-0~20150903+r2013/atac-driver/atac.pl-324-
kmer-0~20150903+r2013/atac-driver/atac.pl:325: #system("ln -s ${seq1}idx $MERYLdir/$id1.fastaidx") if (! -e "$MERYLdir/$id1.fastaidx") && (-e "${seq1}idx");
kmer-0~20150903+r2013/atac-driver/atac.pl:326: #system("ln -s ${seq2}idx $MERYLdir/$id2.fastaidx") if (! -e "$MERYLdir/$id2.fastaidx") && (-e "${seq2}idx");
kmer-0~20150903+r2013/atac-driver/atac.pl-327-
##############################################
kmer-0~20150903+r2013/atac-driver/atac.pl-758- if (! -e "$ATACdir/work/$matches.atac") {
kmer-0~20150903+r2013/atac-driver/atac.pl:759: system("ln -s $ATACdir/work/$matches.matches.extended.chained.gapsclosed.atac $ATACdir/work/$matches.atac");
kmer-0~20150903+r2013/atac-driver/atac.pl-760- }
kmer-0~20150903+r2013/atac-driver/atac.pl-761- if (! -e "$ATACdir/$matches.atac") {
kmer-0~20150903+r2013/atac-driver/atac.pl:762: system("ln $ATACdir/work/$matches.matches.extended.chained.gapsclosed.atac $ATACdir/$matches.atac");
kmer-0~20150903+r2013/atac-driver/atac.pl-763- }
##############################################
kmer-0~20150903+r2013/atac-driver/atac.pl-940-
kmer-0~20150903+r2013/atac-driver/atac.pl:941: if (system($cmd)) {
kmer-0~20150903+r2013/atac-driver/atac.pl-942- return(1);
##############################################
kmer-0~20150903+r2013/meryl/build.C-147- fprintf(F, ". $SGE_ROOT/$SGE_CELL/common/settings.sh\n");
kmer-0~20150903+r2013/meryl/build.C:148: fprintf(F, "batchnum=`expr $SGE_TASK_ID - 1`\n");
kmer-0~20150903+r2013/meryl/build.C-149- fprintf(F, "%s -v -countbatch $batchnum -o %s\n", args->execName, args->outputFile);
##############################################
kmer-0~20150903+r2013/meryl/asmMerQC.sh-47-if [ ! -e $asm.normalcontigs.fasta ] ; then
kmer-0~20150903+r2013/meryl/asmMerQC.sh:48: bin/asmOutputContigsFasta < $dir/9-terminator/$asm.asm > $asm.normalcontigs.fasta &
kmer-0~20150903+r2013/meryl/asmMerQC.sh-49-fi
kmer-0~20150903+r2013/meryl/asmMerQC.sh-50-if [ ! -e $asm.degeneratecontigs.fasta ] ; then
kmer-0~20150903+r2013/meryl/asmMerQC.sh:51: bin/asmOutputContigsFasta -D < $dir/9-terminator/$asm.asm > $asm.degeneratecontigs.fasta &
kmer-0~20150903+r2013/meryl/asmMerQC.sh-52-fi
kmer-0~20150903+r2013/meryl/asmMerQC.sh-53-if [ ! -e $asm.allcontigs.fasta ] ; then
kmer-0~20150903+r2013/meryl/asmMerQC.sh:54: bin/asmOutputContigsFasta -d < $dir/9-terminator/$asm.asm > $asm.allcontigs.fasta &
kmer-0~20150903+r2013/meryl/asmMerQC.sh-55-fi
##############################################
kmer-0~20150903+r2013/libbio/Make.include-63-$/alphabet.h: $/alphabet-generate.c $/alphabet-acgtspace.c $/alphabet-colorspace.c
kmer-0~20150903+r2013/libbio/Make.include:64: $(CC) $(CFLAGS) $(CFLAGS_COMPILE) -o `dirname $@`/a.out $<
kmer-0~20150903+r2013/libbio/Make.include:65: cd `dirname $@` ; ./a.out && rm -f ./a.out
##############################################
kmer-0~20150903+r2013/sim4dbutils/cleanPolishes-experiments/evalThresh.pl-6- print "THRESHOLD = $threshold\n";
kmer-0~20150903+r2013/sim4dbutils/cleanPolishes-experiments/evalThresh.pl:7: system("./splitMatches -qquiet -threshold $threshold < /part3/polishes-good");
kmer-0~20150903+r2013/sim4dbutils/cleanPolishes-experiments/evalThresh.pl-8- $threshold += 10000
##############################################
kmer-0~20150903+r2013/sim4dbutils/Make.include-107- @ echo See page 85 in Big Bad Bri IR#2 for notes on parseSNP-test.
kmer-0~20150903+r2013/sim4dbutils/Make.include:108: @ t=`dirname $<`/test ${SIM4DB/}sim4db -align -cdna $t/parsesnp-snp.fasta -genomic $t/parsesnp-gen.fasta -o $t/parsesnp-sim4.out
kmer-0~20150903+r2013/sim4dbutils/Make.include:109: @ t=`dirname $<`/test $< -O $t/parsesnp-good -F $t/parsesnp-fail < $t/parsesnp-sim4.out
kmer-0~20150903+r2013/sim4dbutils/Make.include:110: @-t=`dirname $<`/test diff $t/parsesnp-good $t/parsesnp-correct-parsed > $t/parsesnp-diffs
kmer-0~20150903+r2013/sim4dbutils/Make.include:111: @ t=`dirname $<`/test; \
kmer-0~20150903+r2013/sim4dbutils/Make.include-112- if test -s $t/parsesnp-diffs ; then \
##############################################
kmer-0~20150903+r2013/sim4dbutils/Make.include-117- echo "parseSNP tests passed" ; \
kmer-0~20150903+r2013/sim4dbutils/Make.include:118: t=`dirname $<` rm -f $t/parsesnp-good $t/parsesnp-fail $t/parsesnp-sim4.out $t/parsesnp-diffs $t/parsesnp-gen.fastaidx $t/parsesnp-snp.fastaidx; \
kmer-0~20150903+r2013/sim4dbutils/Make.include-119- fi
##############################################
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-75-
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:76:system("mkdir $dir") if (! -d $dir);
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-77-die "Can't find '$dir'\n" if (! -d $dir);
##############################################
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-79-if (! -e "$dir/gen/gen.partitioned") {
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:80: system("mkdir $dir/gen") if (! -d "$dir/gen");
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:81: system("$bin/leaff -F $genome --partition $dir/gen/gen $gseg");
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-82- open(F, "> $dir/gen/gen.partitioned");
##############################################
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-86-if (! -e "$dir/qry/qry.partitioned") {
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:87: system("mkdir $dir/qry") if (! -d "$dir/qry");
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:88: system("$bin/leaff -F $query --partition $dir/qry/qry $qseg");
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-89- open(F, "> $dir/qry/qry.partitioned");
##############################################
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-100-print F "#!/bin/sh\n";
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:101:print F "PIECE=`expr \$SGE_TASK_ID - 1`\n";
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:102:print F "GPIECE=`expr \$PIECE % $gen + 1`\n";
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:103:print F "QPIECE=`expr \$PIECE / $gen + 1`\n";
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:104:print F "GPIECE=`printf %03d \$GPIECE`\n";
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:105:print F "QPIECE=`printf %03d \$QPIECE`\n";
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-106-print F "scratchname=/scratch/\$\$-\$GPIECE-\$QPIECE\n";
##############################################
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-156- if (! -e "${_}idx") {
kmer-0~20150903+r2013/snapper/snapper2-sge.pl:157: system("$bin/leaff -F $_");
kmer-0~20150903+r2013/snapper/snapper2-sge.pl-158- }
##############################################
kmer-0~20150903+r2013/snapper/eval/domap14.sh-22-
kmer-0~20150903+r2013/snapper/eval/domap14.sh:23: xx=`expr $nn % 1 + 1`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:24: gn=`echo chr14 | cut -d' ' -f $xx`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:25: nn=`expr $nn / 1`
kmer-0~20150903+r2013/snapper/eval/domap14.sh-26-
kmer-0~20150903+r2013/snapper/eval/domap14.sh:27: xx=`expr $nn % 8 + 1`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:28: fg=`echo f1 f2 f3 f4 f5 f6 f7 f8 | cut -d' ' -f $xx`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:29: nn=`expr $nn / 8`
kmer-0~20150903+r2013/snapper/eval/domap14.sh-30-
kmer-0~20150903+r2013/snapper/eval/domap14.sh:31: xx=`expr $nn % 1 + 1`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:32: ms=`echo 28 | cut -d' ' -f $xx`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:33: nn=`expr $nn / 1`
kmer-0~20150903+r2013/snapper/eval/domap14.sh-34-
kmer-0~20150903+r2013/snapper/eval/domap14.sh:35: xx=`expr $nn % 19 + 1`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:36: mk=`echo 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 | cut -d' ' -f $xx`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:37: nn=`expr $nn / 19`
kmer-0~20150903+r2013/snapper/eval/domap14.sh-38-
kmer-0~20150903+r2013/snapper/eval/domap14.sh:39: xx=`expr $nn % 14 + 1`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:40: ig=`echo 0000 0001 0002 0004 0008 0016 0032 0064 0128 0256 0512 1024 2048 4096 | cut -d' ' -f $xx`
kmer-0~20150903+r2013/snapper/eval/domap14.sh:41: nn=`expr $nn / 14`
kmer-0~20150903+r2013/snapper/eval/domap14.sh-42-
kmer-0~20150903+r2013/snapper/eval/domap14.sh:43: name=`echo $gn.$fg.ms$ms.mk$mk.ig$ig`
kmer-0~20150903+r2013/snapper/eval/domap14.sh-44-}
##############################################
kmer-0~20150903+r2013/snapper/eval/domap14.sh-57- fi
kmer-0~20150903+r2013/snapper/eval/domap14.sh:58: mm=`expr $mm + 1`
kmer-0~20150903+r2013/snapper/eval/domap14.sh-59- done
##############################################
kmer-0~20150903+r2013/snapper/eval/domap14.sh-64-
kmer-0~20150903+r2013/snapper/eval/domap14.sh:65:nn=`expr $SGE_TASK_ID - 1`
kmer-0~20150903+r2013/snapper/eval/domap14.sh-66-decodeJob $nn
##############################################
kmer-0~20150903+r2013/ESTmapper/scheduler.pm-35- } elsif (defined $pid) {
kmer-0~20150903+r2013/ESTmapper/scheduler.pm:36: exec($process); # Child, runs the process
kmer-0~20150903+r2013/ESTmapper/scheduler.pm-37- } elsif ($! =~ /No more processes/) {
##############################################
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-34-
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:35: my $rc = 0xffff & system($cmd);
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-36-
##############################################
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-440-
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:441: my $cdnaInInput = int(`$prog{'leaff'} -F $path/0-input/cDNA.fasta -d`);
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-442-
##############################################
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-490- print F " fi\n";
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:491: print F " jid=`expr \$1 + 1`\n";;
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-492- print F "fi\n";
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-493- print F "\n";
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:494: print F "jid=`head -\$jid $path/0-input/genome/segments | tail -1`\n";
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-495- print F "\n";
##############################################
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-633-
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:634: my $c = int(`wc -l < $path/1-search/$_.count`) if (-e "$path/1-search/$_.count");
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-635-
##############################################
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-817- if ($batchsize == 0) {
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:818: $batchsize = int(`wc -l < $path/2-filter/filteredHits` / $numbatches) + 1;
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-819- $batchsize = 10000 if ($batchsize < 10000);
##############################################
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-857- print F " fi\n";
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:858: print F " jid=`expr \$1 + 1`\n";;
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-859- print F "fi\n";
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-860- print F "\n";
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:861: print F "jid=`head -\$jid $path/3-polish/partitions | tail -1`\n";
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-862- print F "\n";
##############################################
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-1260- print F "cDNA COUNTS:\n";
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:1261: my $cnttotl = int(`grep -c '^>' $path/0-input/cDNA.fasta`);
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:1262: my $cntgood = int(`grep -c '^>' $path/cDNA-good.fasta`);
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:1263: my $cntmiss = int(`grep -c '^>' $path/cDNA-missing.fasta`);
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:1264: my $cntrept = int(`grep -c '^>' $path/cDNA-repeat.fasta`) if (-e "$path/cDNA-repeat.fasta");
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl:1265: my $cntzero = int(`grep -c '^>' $path/cDNA-zero.fasta`);
kmer-0~20150903+r2013/ESTmapper/ESTmapper.pl-1266-
##############################################
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-36-
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl:37: my $rc = 0xffff & system($cmd);
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-38-
##############################################
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-143-
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl:144:system("mkdir -p $genomedir") if (! -d $genomedir);
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-145-
##############################################
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-260-print F "fi\n";
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl:261:print F "jobp=`cat $genomedir/create.dat | head -n \$jobid | tail -n 1`\n";
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-262-print F "\n";
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl:263:print F "seg=`echo \$jobp | awk '{ print \$1 }'`\n";
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl:264:print F "beg=`echo \$jobp | awk '{ print \$2 }'`\n";
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl:265:print F "end=`echo \$jobp | awk '{ print \$3 }'`\n";
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-266-print F "\n";
##############################################
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-281-print F "\n";
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl:282:print F "bat=`expr \$jobid - 1`\n";
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-283-print F "\n";
##############################################
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-351-
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl:352: system("mkdir $genomedir/sgeout") if (! -d "$genomedir/sgeout");
kmer-0~20150903+r2013/ESTmapper/configureESTmapper.pl-353-
##############################################
kmer-0~20150903+r2013/debian/patches/2to3.patch-1657- echo "Python executable found in '$PYTHON'"
kmer-0~20150903+r2013/debian/patches/2to3.patch:1658:- CFLAGS_PYTHON=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_inc()"`
kmer-0~20150903+r2013/debian/patches/2to3.patch:1659:+ CFLAGS_PYTHON=`$PYTHON -c "from distutils import sysconfig; print(sysconfig.get_python_inc())"`
kmer-0~20150903+r2013/debian/patches/2to3.patch-1660-
##############################################
kmer-0~20150903+r2013/.pc/allow-freebsd-build.patch/configure.sh-89- echo "Python executable found in '$PYTHON'"
kmer-0~20150903+r2013/.pc/allow-freebsd-build.patch/configure.sh:90: CFLAGS_PYTHON=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_inc()"`
kmer-0~20150903+r2013/.pc/allow-freebsd-build.patch/configure.sh-91-
##############################################
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-253-
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:254: system("mkdir $ATACdir") if (! -d "$ATACdir");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:255: system("mkdir $ATACdir/work") if (! -d "$ATACdir/work");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:256: system("mkdir $ATACdir/stats") if (! -d "$ATACdir/stats");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:257: system("mkdir $MERYLdir") if (! -d "$MERYLdir");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-258-}
##############################################
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-320-
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:321: #system("ln -s $seq1 $MERYLdir/$id1.fasta") if (! -e "$MERYLdir/$id1.fasta");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:322: #system("ln -s $seq2 $MERYLdir/$id2.fasta") if (! -e "$MERYLdir/$id2.fasta");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-323-
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:324: #system("ln -s ${seq1}idx $MERYLdir/$id1.fastaidx") if (! -e "$MERYLdir/$id1.fastaidx") && (-e "${seq1}idx");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:325: #system("ln -s ${seq2}idx $MERYLdir/$id2.fastaidx") if (! -e "$MERYLdir/$id2.fastaidx") && (-e "${seq2}idx");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-326-
##############################################
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-757- if (! -e "$ATACdir/work/$matches.atac") {
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:758: system("ln -s $ATACdir/work/$matches.matches.extended.chained.gapsclosed.atac $ATACdir/work/$matches.atac");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-759- }
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-760- if (! -e "$ATACdir/$matches.atac") {
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:761: system("ln $ATACdir/work/$matches.matches.extended.chained.gapsclosed.atac $ATACdir/$matches.atac");
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-762- }
##############################################
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-939-
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl:940: if (system($cmd)) {
kmer-0~20150903+r2013/.pc/atac-helper-script-paths.patch/atac-driver/atac.pl-941- return(1);
##############################################
kmer-0~20150903+r2013/.pc/linux-cflags.patch/configure.sh-89- echo "Python executable found in '$PYTHON'"
kmer-0~20150903+r2013/.pc/linux-cflags.patch/configure.sh:90: CFLAGS_PYTHON=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_inc()"`
kmer-0~20150903+r2013/.pc/linux-cflags.patch/configure.sh-91-
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-549-$/.all:
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:550: cd `dirname $@` && ${MAKE} all
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-551-
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-552-$/.real-clean $/.clean:
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:553: cd `dirname $@` && ${MAKE} clean
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-554-
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-880- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:881: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-882- echo ":Copying $$$${F} to $$$${Fout}:" ; \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:883: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-884- rm -f $$$${Fout} && cp -fp $$$${F} $$$${Fout} ; \
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-895- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:896: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-897- echo ":Copying $$$${F}${.EXE} to $$$${Fout}${.EXE}:" ; \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:898: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-899- rm -f $$$${Fout}${.EXE} && cp -fp $$$${F}${.EXE} $$$${Fout}${.EXE} ; \
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-910- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:911: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-912- echo ":Mangling $$$${F} to $$$${Fout}:" ; \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:913: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-914- rm -f $$$${Fout} && cp -fp $$$${F} $$$${Fout} ; \
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-946- @ echo "making $@"
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:947: dir=`echo $< | sed -e's~[^/]*$$~~'`; \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-948- ${CCDEP} ${CDEPFLAGS} ${CFLAGS} $< | \
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-954- @ echo "making $@"
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:955: dir=`echo $< | sed -e's~[^/]*$$~~'`; \
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-956- ${CXXDEP} ${CXXDEPFLAGS} ${CXXFLAGS} $< | \
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-1090-%.dvi: %.tex
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:1091: ${-LATEX} cd `dirname $<` && ${LATEX} `basename $<` && ${LATEX} `basename $<`
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-1092-
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-1093-%.aux: %.tex
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:1094: ${-LATEX} cd `dirname $<` && ${LATEX} `basename $<` && ${LATEX} `basename $<`
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-1095-
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-1096-%.bbl: %.aux
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:1097: ${-LATEX} cd `dirname $<` && ${BIBTEX} `basename ${<:.aux=}`
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-1098-</pre>
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-1106-${ALL_TEX_PS} ${ALL_TEX_PDF:.pdf=.ps}: %.ps: %.dvi
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki:1107: ${-LATEX} cd `dirname $<` && ${DVIPS} -o `basename $@` `basename $<`
kmer-0~20150903+r2013/.pc/2to3.patch/Makefile.wiki-1108-
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-254-
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:255: system("mkdir $ATACdir") if (! -d "$ATACdir");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:256: system("mkdir $ATACdir/work") if (! -d "$ATACdir/work");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:257: system("mkdir $ATACdir/stats") if (! -d "$ATACdir/stats");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:258: system("mkdir $MERYLdir") if (! -d "$MERYLdir");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-259-}
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-321-
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:322: #system("ln -s $seq1 $MERYLdir/$id1.fasta") if (! -e "$MERYLdir/$id1.fasta");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:323: #system("ln -s $seq2 $MERYLdir/$id2.fasta") if (! -e "$MERYLdir/$id2.fasta");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-324-
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:325: #system("ln -s ${seq1}idx $MERYLdir/$id1.fastaidx") if (! -e "$MERYLdir/$id1.fastaidx") && (-e "${seq1}idx");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:326: #system("ln -s ${seq2}idx $MERYLdir/$id2.fastaidx") if (! -e "$MERYLdir/$id2.fastaidx") && (-e "${seq2}idx");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-327-
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-758- if (! -e "$ATACdir/work/$matches.atac") {
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:759: system("ln -s $ATACdir/work/$matches.matches.extended.chained.gapsclosed.atac $ATACdir/work/$matches.atac");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-760- }
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-761- if (! -e "$ATACdir/$matches.atac") {
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:762: system("ln $ATACdir/work/$matches.matches.extended.chained.gapsclosed.atac $ATACdir/$matches.atac");
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-763- }
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-940-
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl:941: if (system($cmd)) {
kmer-0~20150903+r2013/.pc/2to3.patch/atac-driver/atac.pl-942- return(1);
##############################################
kmer-0~20150903+r2013/.pc/2to3.patch/configure.sh-89- echo "Python executable found in '$PYTHON'"
kmer-0~20150903+r2013/.pc/2to3.patch/configure.sh:90: CFLAGS_PYTHON=`$PYTHON -c "from distutils import sysconfig; print sysconfig.get_python_inc()"`
kmer-0~20150903+r2013/.pc/2to3.patch/configure.sh-91-
##############################################
kmer-0~20150903+r2013/Makefile.wiki-549-$/.all:
kmer-0~20150903+r2013/Makefile.wiki:550: cd `dirname $@` && ${MAKE} all
kmer-0~20150903+r2013/Makefile.wiki-551-
kmer-0~20150903+r2013/Makefile.wiki-552-$/.real-clean $/.clean:
kmer-0~20150903+r2013/Makefile.wiki:553: cd `dirname $@` && ${MAKE} clean
kmer-0~20150903+r2013/Makefile.wiki-554-
##############################################
kmer-0~20150903+r2013/Makefile.wiki-880- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/Makefile.wiki:881: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/Makefile.wiki-882- echo ":Copying $$$${F} to $$$${Fout}:" ; \
kmer-0~20150903+r2013/Makefile.wiki:883: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/Makefile.wiki-884- rm -f $$$${Fout} && cp -fp $$$${F} $$$${Fout} ; \
##############################################
kmer-0~20150903+r2013/Makefile.wiki-895- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/Makefile.wiki:896: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/Makefile.wiki-897- echo ":Copying $$$${F}${.EXE} to $$$${Fout}${.EXE}:" ; \
kmer-0~20150903+r2013/Makefile.wiki:898: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/Makefile.wiki-899- rm -f $$$${Fout}${.EXE} && cp -fp $$$${F}${.EXE} $$$${Fout}${.EXE} ; \
##############################################
kmer-0~20150903+r2013/Makefile.wiki-910- for D in $$$${dirs} ; do \
kmer-0~20150903+r2013/Makefile.wiki:911: Fout=$${INSTALL/}$$$${D}`basename $$$${F}` ; \
kmer-0~20150903+r2013/Makefile.wiki-912- echo ":Mangling $$$${F} to $$$${Fout}:" ; \
kmer-0~20150903+r2013/Makefile.wiki:913: mkdir -p `dirname $$$${Fout}` && \
kmer-0~20150903+r2013/Makefile.wiki-914- rm -f $$$${Fout} && cp -fp $$$${F} $$$${Fout} ; \
##############################################
kmer-0~20150903+r2013/Makefile.wiki-946- @ echo "making $@"
kmer-0~20150903+r2013/Makefile.wiki:947: dir=`echo $< | sed -e's~[^/]*$$~~'`; \
kmer-0~20150903+r2013/Makefile.wiki-948- ${CCDEP} ${CDEPFLAGS} ${CFLAGS} $< | \
##############################################
kmer-0~20150903+r2013/Makefile.wiki-954- @ echo "making $@"
kmer-0~20150903+r2013/Makefile.wiki:955: dir=`echo $< | sed -e's~[^/]*$$~~'`; \
kmer-0~20150903+r2013/Makefile.wiki-956- ${CXXDEP} ${CXXDEPFLAGS} ${CXXFLAGS} $< | \
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kmer-0~20150903+r2013/Makefile.wiki-1090-%.dvi: %.tex
kmer-0~20150903+r2013/Makefile.wiki:1091: ${-LATEX} cd `dirname $<` && ${LATEX} `basename $<` && ${LATEX} `basename $<`
kmer-0~20150903+r2013/Makefile.wiki-1092-
kmer-0~20150903+r2013/Makefile.wiki-1093-%.aux: %.tex
kmer-0~20150903+r2013/Makefile.wiki:1094: ${-LATEX} cd `dirname $<` && ${LATEX} `basename $<` && ${LATEX} `basename $<`
kmer-0~20150903+r2013/Makefile.wiki-1095-
kmer-0~20150903+r2013/Makefile.wiki-1096-%.bbl: %.aux
kmer-0~20150903+r2013/Makefile.wiki:1097: ${-LATEX} cd `dirname $<` && ${BIBTEX} `basename ${<:.aux=}`
kmer-0~20150903+r2013/Makefile.wiki-1098-</pre>
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kmer-0~20150903+r2013/Makefile.wiki-1106-${ALL_TEX_PS} ${ALL_TEX_PDF:.pdf=.ps}: %.ps: %.dvi
kmer-0~20150903+r2013/Makefile.wiki:1107: ${-LATEX} cd `dirname $<` && ${DVIPS} -o `basename $@` `basename $<`
kmer-0~20150903+r2013/Makefile.wiki-1108-
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kmer-0~20150903+r2013/configure.sh-89- echo "Python executable found in '$PYTHON'"
kmer-0~20150903+r2013/configure.sh:90: CFLAGS_PYTHON=`$PYTHON -c "from distutils import sysconfig; print(sysconfig.get_python_inc())"`
kmer-0~20150903+r2013/configure.sh-91-