From 558f18b319df9294e35548e51187b050ccbaae35 Mon Sep 17 00:00:00 2001 From: jschauma Date: Sat, 4 Oct 2003 19:13:28 +0000 Subject: 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. --- biology/xylem/DESCR | 3 + biology/xylem/Makefile | 37 ++++++++++ biology/xylem/PLIST | 51 ++++++++++++++ biology/xylem/distinfo | 6 ++ biology/xylem/patches/patch-aa | 149 +++++++++++++++++++++++++++++++++++++++++ biology/xylem/patches/patch-ab | 76 +++++++++++++++++++++ 6 files changed, 322 insertions(+) create mode 100644 biology/xylem/DESCR create mode 100644 biology/xylem/Makefile create mode 100644 biology/xylem/PLIST create mode 100644 biology/xylem/distinfo create mode 100644 biology/xylem/patches/patch-aa create mode 100644 biology/xylem/patches/patch-ab (limited to 'biology') 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 temp.ref ++ reform -g -p -c -fi 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 temp.pep ++ ribosome 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 temp.prot2nuc ++ prot2nuc 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 temp.dbstat ++ dbstat 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 temp.interleaved.phylip ++ flat2phyl 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 temp.sequential.phylip ++ flat2phyl -s 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 temp.shuf ++ shuffle -s3456 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 + -- cgit v1.2.3