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authorjschauma <jschauma>2003-10-04 19:13:28 +0000
committerjschauma <jschauma>2003-10-04 19:13:28 +0000
commit8bb1cda5b0236f1867156e5cafccb7ae5a346dbb (patch)
tree8cea07310eca5f1e40385a76e7bf7494cf219e3b /biology
parent5a1b2e86ef167a0cf61ba1deb22eca1815661cdf (diff)
downloadpkgsrc-8bb1cda5b0236f1867156e5cafccb7ae5a346dbb.tar.gz
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.
Diffstat (limited to 'biology')
-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
+