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-rw-r--r--biology/xylem/DESCR3
-rw-r--r--biology/xylem/Makefile37
-rw-r--r--biology/xylem/PLIST51
-rw-r--r--biology/xylem/distinfo6
-rw-r--r--biology/xylem/patches/patch-aa149
-rw-r--r--biology/xylem/patches/patch-ab76
6 files changed, 322 insertions, 0 deletions
diff --git a/biology/xylem/DESCR b/biology/xylem/DESCR
new file mode 100644
index 00000000000..095ffe9b89e
--- /dev/null
+++ b/biology/xylem/DESCR
@@ -0,0 +1,3 @@
+XYLEM is a package of tools designed to exploit the Unix environment to enable
+the user to identify, extract and manipulate data from major databases such as
+GenBank, EMBL and PIR.
diff --git a/biology/xylem/Makefile b/biology/xylem/Makefile
new file mode 100644
index 00000000000..81560ebe373
--- /dev/null
+++ b/biology/xylem/Makefile
@@ -0,0 +1,37 @@
+# $NetBSD: Makefile,v 1.1.1.1 2003/10/04 19:13:28 jschauma Exp $
+#
+
+DISTNAME= xylem.1.8.7
+PKGNAME= xylem-1.8.7
+WRKSRC= ${WRKDIR}/xylem/src.c
+CATEGORIES= biology
+MASTER_SITES= ftp://ftp.cc.umanitoba.ca/psgendb/
+EXTRACT_SUFX= .tar.Z
+
+MAINTAINER= hdp@cs.nmsu.edu
+HOMEPAGE= http://home.cc.umanitoba.ca/~psgendb/XYLEM.html
+COMMENT= Tools for manipulation of genetic databases
+
+USE_BUILDLINK2= YES
+
+do-configure:
+ ${CP} ${WRKSRC}/p2c.h.standard ${WRKSRC}/p2c.h
+
+# Rename some binaries to avoid confusion with base system or conflicts
+post-build:
+ ${RM} -f ${WRKSRC}/../test/testxylem.csh.orig
+ ${MV} ${WRKSRC}/identify ${WRKSRC}/xyl-identify
+ ${MV} ${WRKSRC}/shuffle ${WRKSRC}/xyl-shuffle
+
+do-install:
+.for PROGRAM in dbstat getloc getob xyl-identify prot2nuc reform ribosome \
+ splitdb xyl-shuffle flat2phyl phyl2flat
+ ${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin
+.endfor
+ ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/xylem
+ ${INSTALL_DATA} ${WRKSRC}/../doc/* ${PREFIX}/share/doc/xylem/
+ ${INSTALL_DATA_DIR} ${PREFIX}/share/examples/xylem
+ ${INSTALL_DATA} ${WRKSRC}/../test/sample.* ${PREFIX}/share/examples/xylem
+ ${INSTALL_SCRIPT} ${WRKSRC}/../test/testxylem.csh ${PREFIX}/share/examples/xylem
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/xylem/PLIST b/biology/xylem/PLIST
new file mode 100644
index 00000000000..a0dc0796a6f
--- /dev/null
+++ b/biology/xylem/PLIST
@@ -0,0 +1,51 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2003/10/04 19:13:30 jschauma Exp $
+bin/dbstat
+bin/flat2phyl
+bin/getloc
+bin/getob
+bin/phyl2flat
+bin/prot2nuc
+bin/reform
+bin/ribosome
+bin/splitdb
+bin/xyl-identify
+bin/xyl-shuffle
+share/doc/xylem/clu2ig.asc
+share/doc/xylem/dbstat.asc
+share/doc/xylem/features.asc
+share/doc/xylem/fetch.asc
+share/doc/xylem/findkey.asc
+share/doc/xylem/flat2phyl.asc
+share/doc/xylem/getloc.asc
+share/doc/xylem/getob.asc
+share/doc/xylem/identify.asc
+share/doc/xylem/phyl2flat.asc
+share/doc/xylem/printdoc.asc
+share/doc/xylem/prot2nuc.asc
+share/doc/xylem/reform.asc
+share/doc/xylem/ribosome.asc
+share/doc/xylem/shuffle.asc
+share/doc/xylem/splitdb.asc
+share/doc/xylem/xylem.asc
+share/examples/xylem/sample.aln
+share/examples/xylem/sample.ano
+share/examples/xylem/sample.dbstat
+share/examples/xylem/sample.exp
+share/examples/xylem/sample.flat
+share/examples/xylem/sample.fnd
+share/examples/xylem/sample.gen
+share/examples/xylem/sample.ind
+share/examples/xylem/sample.inp
+share/examples/xylem/sample.interleaved.phylip
+share/examples/xylem/sample.msg
+share/examples/xylem/sample.nam
+share/examples/xylem/sample.out
+share/examples/xylem/sample.pep
+share/examples/xylem/sample.pro
+share/examples/xylem/sample.prot2nuc
+share/examples/xylem/sample.ref
+share/examples/xylem/sample.sequential.phylip
+share/examples/xylem/sample.wrp
+share/examples/xylem/testxylem.csh
+@dirrm share/examples/xylem
+@dirrm share/doc/xylem
diff --git a/biology/xylem/distinfo b/biology/xylem/distinfo
new file mode 100644
index 00000000000..05b51f4f2ec
--- /dev/null
+++ b/biology/xylem/distinfo
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1.1.1 2003/10/04 19:13:30 jschauma Exp $
+
+SHA1 (xylem.1.8.7.tar.Z) = 7816507d576448ff15659fef744dd27cc64562f5
+Size (xylem.1.8.7.tar.Z) = 417985 bytes
+SHA1 (patch-aa) = 10d990c940e4283e8dad1e3280b9abd70f0300d0
+SHA1 (patch-ab) = 8c45aa95e082a64b2ca6a4049fe6a57ce1cb42d5
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 = $status
diff --git a/biology/xylem/patches/patch-ab b/biology/xylem/patches/patch-ab
new file mode 100644
index 00000000000..274bffe0159
--- /dev/null
+++ b/biology/xylem/patches/patch-ab
@@ -0,0 +1,76 @@
+$NetBSD: patch-ab,v 1.1.1.1 2003/10/04 19:13:33 jschauma Exp $
+
+--- Makefile.orig 2000-08-17 12:17:18.000000000 -0400
++++ Makefile 2003-09-28 17:05:26.000000000 -0400
+@@ -6,9 +6,9 @@
+ LDLIB = .
+ LIBOBJS = p2clib.o
+ #CC= gcc
+-CC= cc
+-CFLAGS= -O -L$(LDLIB) -lp2c -lm -I$(INCLIB)
+-LFLAGS= -c
++#CC= cc
++MYCFLAGS= -O -L$(LDLIB) -lp2c -lm -I$(INCLIB)
++LFLAGS+= -c
+
+ PROGS= dbstat getloc getob identify prot2nuc reform ribosome splitdb shuffle flat2phyl phyl2flat
+
+@@ -22,45 +22,45 @@
+
+ # Making the p2c runtime library
+ libp2c.a: $(LIBOBJS)
+- ar r libp2c.a $(LIBOBJS); ranlib libp2c.a
++ ${AR} r libp2c.a $(LIBOBJS); ranlib libp2c.a
+
+ p2clib.o: p2clib.c
+- $(CC) $(LFLAGS) p2clib.c
++ $(CC) $(LFLAGS) ${CFLAGS} p2clib.c
+
+ #libp2c.a: libp2c.a
+ # ranlib libp2c.a
+
+ # Making the programs
+ dbstat :
+- $(CC) dbstat.c $(CFLAGS) -o dbstat
++ $(CC) dbstat.c $(MYCFLAGS) ${CFLAGS} -o dbstat
+
+ flat2phyl :
+- $(CC) flat2phyl.c $(CFLAGS) -o flat2phyl
++ $(CC) flat2phyl.c $(MYCFLAGS) ${CFLAGS} -o flat2phyl
+
+ phyl2flat :
+- $(CC) phyl2flat.c $(CFLAGS) -o phyl2flat
++ $(CC) phyl2flat.c $(MYCFLAGS) ${CFLAGS} -o phyl2flat
+
+ getloc :
+- $(CC) getloc.c $(CFLAGS) -o getloc
++ $(CC) getloc.c $(MYCFLAGS) ${CFLAGS} -o getloc
+
+ getob :
+- $(CC) getob.c $(CFLAGS) -o getob
++ $(CC) getob.c $(MYCFLAGS) ${CFLAGS} -o getob
+
+ identify :
+- $(CC) identify.c $(CFLAGS) -o identify
++ $(CC) identify.c $(MYCFLAGS) ${CFLAGS} -o identify
+
+ prot2nuc :
+- $(CC) prot2nuc.c $(CFLAGS) -o prot2nuc
++ $(CC) prot2nuc.c $(MYCFLAGS) ${CFLAGS} -o prot2nuc
+
+ reform :
+- $(CC) reform.c $(CFLAGS) -o reform
++ $(CC) reform.c $(MYCFLAGS) ${CFLAGS} -o reform
+
+ ribosome :
+- $(CC) ribosome.c $(CFLAGS) -o ribosome
++ $(CC) ribosome.c $(MYCFLAGS) ${CFLAGS} -o ribosome
+
+ shuffle :
+- $(CC) shuffle.c $(CFLAGS) -o shuffle
++ $(CC) shuffle.c $(MYCFLAGS) ${CFLAGS} -o shuffle
+
+ splitdb :
+- $(CC) splitdb.c $(CFLAGS) -o splitdb
++ $(CC) splitdb.c $(MYCFLAGS) ${CFLAGS} -o splitdb
+
generated by cgit v1.2.3 (git 2.39.1) at 2024-12-22 13:41:25 +0000