Initial import of xylem, one of the many packages provided by

brook at biology dot nmsu dot edu and his team at NMSU.

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.

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 
+