diff options
Diffstat (limited to 'biology/xylem/patches/patch-aa')
| -rw-r--r-- | biology/xylem/patches/patch-aa | 149 |
1 files changed, 149 insertions, 0 deletions
diff --git a/biology/xylem/patches/patch-aa b/biology/xylem/patches/patch-aa new file mode 100644 index 00000000000..7dc52e93605 --- /dev/null +++ b/biology/xylem/patches/patch-aa @@ -0,0 +1,149 @@ +$NetBSD: patch-aa,v 1.1.1.1 2003/10/04 19:13:31 jschauma Exp $ + +--- ../test/testxylem.csh.orig 2001-08-18 16:31:51.000000000 -0400 ++++ ../test/testxylem.csh 2003-09-28 17:29:21.000000000 -0400 +@@ -10,13 +10,12 @@ + # set default parameters + ##################################################################### + set RM = rm +-set BINDIR = ../bin + + # set $testset to programs to be tested. + set NUMARGS = $#argv + + if ($NUMARGS == 0) then +- set TESTSET = (splitdb getloc identify getob reform ribosome shuffle\ ++ set TESTSET = (splitdb getloc xyl-identify getob reform ribosome shuffle\ + dbstat flat2phyl findkey fetch features) + else + set TESTSET = $1 +@@ -31,7 +30,7 @@ + ######### splitdb ####### + case splitdb: + # run the program +- $BINDIR/splitdb sample.gen temp.ano temp.wrp temp.ind ++ splitdb sample.gen temp.ano temp.wrp temp.ind + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -73,7 +72,7 @@ + ######### getloc ####### + case getloc: + # run the program +- $BINDIR/getloc sample.nam sample.ano sample.wrp sample.ind temp.gen ++ getloc sample.nam sample.ano sample.wrp sample.ind temp.gen + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -95,10 +94,10 @@ + breaksw + + ######### identify ####### +- case identify: ++ case xyl-identify: + # run the program + egrep -n -i LOCUS sample.ano >temp.egrep +- $BINDIR/identify temp.egrep sample.ind temp.nam temp.fnd ++ xyl-identify temp.egrep sample.ind temp.nam temp.fnd + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -132,7 +131,7 @@ + ######### getob ####### + case getob: + # run the program +- $BINDIR/getob sample.inp sample.nam sample.ano sample.wrp sample.ind\ ++ getob sample.inp sample.nam sample.ano sample.wrp sample.ind\ + temp.getob.msg temp.getob.out temp.getob.exp + + # if successful, compare sample files with new output +@@ -175,7 +174,7 @@ + ######### reform ####### + case reform: + # run the program +- $BINDIR/reform -g -p -c -fi <sample.aln > temp.ref ++ reform -g -p -c -fi <sample.aln > temp.ref + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -199,7 +198,7 @@ + ######### ribosome ####### + case ribosome: + # run the program +- $BINDIR/ribosome <sample.out > temp.pep ++ ribosome <sample.out > temp.pep + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -223,7 +222,7 @@ + ######### prot2nuc ####### + case prot2nuc: + # run the program +- $BINDIR/prot2nuc <sample.pro > temp.prot2nuc ++ prot2nuc <sample.pro > temp.prot2nuc + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -247,7 +246,7 @@ + ######### dbstat ####### + case dbstat: + # run the program +- $BINDIR/dbstat <sample.pep > temp.dbstat ++ dbstat <sample.pep > temp.dbstat + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -272,7 +271,7 @@ + case flat2phyl: + + # check results for interleaved format +- $BINDIR/flat2phyl <sample.flat > temp.interleaved.phylip ++ flat2phyl <sample.flat > temp.interleaved.phylip + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -295,7 +294,7 @@ + endif + + # check results for sequential format +- $BINDIR/flat2phyl -s <sample.flat > temp.sequential.phylip ++ flat2phyl -s <sample.flat > temp.sequential.phylip + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -321,7 +320,7 @@ + ######### shuffle ####### + case shuffle: + # run the program +- $BINDIR/shuffle -s3456 <sample.out > temp.shuf ++ shuffle -s3456 <sample.out > temp.shuf + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -337,7 +336,7 @@ + case findkey: + # run the program + echo "LOCUS" > temp.kw +- $BINDIR/findkey -G sample.ano temp.kw temp.nam temp.fnd ++ findkey -G sample.ano temp.kw temp.nam temp.fnd + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -371,7 +370,7 @@ + ######### fetch ####### + case fetch: + # run the program +- $BINDIR/fetch -G sample sample.nam temp.gen ++ fetch -G sample sample.nam temp.gen + + # if successful, compare sample files with new output + set SUCCESS = $status +@@ -396,7 +395,7 @@ + case features: + # run the program + cp sample.exp temp.exp +- $BINDIR/features -u sample -E temp.exp ++ features -u sample -E temp.exp + + # if successful, compare sample files with new output + set SUCCESS = $status |