diff --git a/biology/Makefile b/biology/Makefile index 880d5e36e467..52ca8f84d005 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -11,6 +11,7 @@ SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += gaussian98 + SUBDIR += gp SUBDIR += gperiodic SUBDIR += hmmer SUBDIR += kinemage diff --git a/biology/gp/Makefile b/biology/gp/Makefile new file mode 100644 index 000000000000..088119d8fec1 --- /dev/null +++ b/biology/gp/Makefile @@ -0,0 +1,36 @@ +# ex:ts=8 +# New ports collection makefile for: gp +# Date created: Feb 28, 2001 +# Whom: Ying-Chieh Liao +# +# $FreeBSD$ +# + +PORTNAME= gp +PORTVERSION= 0.25 +CATEGORIES= biology +MASTER_SITES= http://www.bioinformatics.org/genpak/download/ +EXTRACT_SUFX= .tgz + +MAINTAINER= ijliao@FreeBSD.org + +LIB_DEPENDS= gd.1:${PORTSDIR}/graphics/gd \ + png.4:${PORTSDIR}/graphics/png + +USE_GMAKE= yes + +MAN1= Genpak.1 gp_acc.1 gp_cusage.1 gp_digest.1 gp_dimer.1 gp_findorf.1 \ + gp_gc.1 gp_getseq.1 gp_matrix.1 gp_mkmtx.1 gp_pattern.1 gp_qs.1 \ + gp_randseq.1 gp_seq2prot.1 gp_slen.1 gp_tm.1 gp_trimer.1 gp_primer.1 + +.if !defined(NOPORTDOCS) +INSTALL_TARGET= install docs +.endif + +post-patch: + @${PERL} -pi -e "s|%%PREFIX%%|${PREFIX}|g ; \ + s|%%MANPREFIX%%|${MANPREFIX}|g ; \ + s|%%DOCDIR%%|${PREFIX}/share/doc|g ; \ + s|%%CFLAGS%%|${CFLAGS}|g" ${WRKSRC}/Makefile + +.include diff --git a/biology/gp/distinfo b/biology/gp/distinfo new file mode 100644 index 000000000000..1d640501a87b --- /dev/null +++ b/biology/gp/distinfo @@ -0,0 +1 @@ +MD5 (gp-0.25.tgz) = 35bc282e2da3d5af24cf44ed01a04551 diff --git a/biology/gp/files/patch-Makefile b/biology/gp/files/patch-Makefile new file mode 100644 index 000000000000..db0ffe3ad507 --- /dev/null +++ b/biology/gp/files/patch-Makefile @@ -0,0 +1,51 @@ +--- Makefile.orig Tue Feb 13 22:41:12 2001 ++++ Makefile Wed Feb 28 01:01:15 2001 +@@ -5,15 +5,13 @@ + ###################################################################### + # Change the following to suit your needs + +-SHELL=/bin/bash +- + # The directory root of your installation + # If you make a personal installation, change it to your home directory + # Default: /usr + # uncomment the following line to install to the default directories... + # TREE=/usr + # ...or the following line to install into your home directory: +-TREE=$(HOME) ++TREE=%%PREFIX%% + + # if you don't have the gd graphic library installed, you have to comment out or + # delete the following line. However, gp_map is such a nice program, so you +@@ -25,7 +23,7 @@ + BINDIR=$(TREE)/bin + + # directory to install the manual pages +-MANDIR=$(TREE)/man ++MANDIR=%%MANPREFIX%%/man + + #directory to install the data directory + DATADIR=$(TREE)/lib +@@ -36,11 +34,11 @@ + # A catalog will be created: $(DOCDIR)/gp + # It will *not* be uninstalled automagically after a "make uninstall" + +-DOCDIR=$(TREE)/doc ++DOCDIR=%%DOCDIR%% + + # Your favourite ANSI compiler and it's flags + CC=gcc +-CFLAGS=-ansi -pedantic -O3 ++CFLAGS=%%CFLAGS%% + + ###################################################################### + # Do not change anything below this line +@@ -58,7 +56,7 @@ + mporfs.seq + + all: +- cd src ; make PROGRAMS="$(PROGRAMS)" GDPROGRAMS="$(GDPROGRAMS)" CC=$(CC) \ ++ cd src ; gmake PROGRAMS="$(PROGRAMS)" GDPROGRAMS="$(GDPROGRAMS)" CC=$(CC) \ + LIBS="$(LIBS)" CFLAGS="$(CFLAGS)" ; + @echo -e "\nAll programs compiled. \nType 'make install' to install all programs." + diff --git a/biology/gp/files/patch-src::Makefile b/biology/gp/files/patch-src::Makefile new file mode 100644 index 000000000000..345fb413bb5b --- /dev/null +++ b/biology/gp/files/patch-src::Makefile @@ -0,0 +1,10 @@ +--- src/Makefile.orig Wed Feb 28 01:01:24 2001 ++++ src/Makefile Wed Feb 28 01:01:31 2001 +@@ -5,7 +5,6 @@ + ###################################################################### + # Change the following to suit your needs + +-SHELL=/bin/bash + CC=gcc + LIBS= -lz -lm + #CFLAGS= -DNLS -DGZ diff --git a/biology/gp/pkg-comment b/biology/gp/pkg-comment new file mode 100644 index 000000000000..c8710a783594 --- /dev/null +++ b/biology/gp/pkg-comment @@ -0,0 +1 @@ +GP is a set of small utilities to manipulate DNA sequences diff --git a/biology/gp/pkg-descr b/biology/gp/pkg-descr new file mode 100644 index 000000000000..a8f362329a99 --- /dev/null +++ b/biology/gp/pkg-descr @@ -0,0 +1,9 @@ +GP is a set of small utilities written in ANSI C to manipulate DNA +sequences in a Unix fashion, fit for combining within shell and cgi +scripts. + +The sequences are usually in fasta format, that means the first line +is the sequence name starting with ">", and the sequence comes in the +next lines. The programs accept also gzipped sequence files. + +WWW: http://www.bioinformatics.org/genpak/#gp diff --git a/biology/gp/pkg-plist b/biology/gp/pkg-plist new file mode 100644 index 000000000000..07c9bb039bf9 --- /dev/null +++ b/biology/gp/pkg-plist @@ -0,0 +1,54 @@ +bin/gp_acc +bin/gp_cusage +bin/gp_digest +bin/gp_dimer +bin/gp_findorf +bin/gp_gc +bin/gp_getseq +bin/gp_matrix +bin/gp_mkmtx +bin/gp_pars +bin/gp_pattern +bin/gp_primer +bin/gp_qs +bin/gp_randseq +bin/gp_scan +bin/gp_seq2prot +bin/gp_shift +bin/gp_slen +bin/gp_tm +bin/gp_trimer +lib/genpak/ecoli.mtx +lib/genpak/enzyme.enz +lib/genpak/mporfs.seq +lib/genpak/myco.cdn +lib/genpak/sample.seq +lib/genpak/standard.cdn +@dirrm lib/genpak +%%PORTDOCS%%share/doc/gp/CHANGES.TXT +%%PORTDOCS%%share/doc/gp/INSTALL.TXT +%%PORTDOCS%%share/doc/gp/LICENSE.TXT +%%PORTDOCS%%share/doc/gp/Makefile +%%PORTDOCS%%share/doc/gp/README.TXT +%%PORTDOCS%%share/doc/gp/html/README.html +%%PORTDOCS%%share/doc/gp/html/gp_acc.html +%%PORTDOCS%%share/doc/gp/html/gp_cusage.html +%%PORTDOCS%%share/doc/gp/html/gp_digest.html +%%PORTDOCS%%share/doc/gp/html/gp_dimer.html +%%PORTDOCS%%share/doc/gp/html/gp_findorf.html +%%PORTDOCS%%share/doc/gp/html/gp_gc.html +%%PORTDOCS%%share/doc/gp/html/gp_getseq.html +%%PORTDOCS%%share/doc/gp/html/gp_map.html +%%PORTDOCS%%share/doc/gp/html/gp_matrix.html +%%PORTDOCS%%share/doc/gp/html/gp_mkmtx.html +%%PORTDOCS%%share/doc/gp/html/gp_pattern.html +%%PORTDOCS%%share/doc/gp/html/gp_primer.html +%%PORTDOCS%%share/doc/gp/html/gp_qs.html +%%PORTDOCS%%share/doc/gp/html/gp_randseq.html +%%PORTDOCS%%share/doc/gp/html/gp_seq2prot.html +%%PORTDOCS%%share/doc/gp/html/gp_slen.html +%%PORTDOCS%%share/doc/gp/html/gp_tm.html +%%PORTDOCS%%share/doc/gp/html/gp_trimer.html +%%PORTDOCS%%share/doc/gp/html/index.html +%%PORTDOCS%%@dirrm share/doc/gp/html +%%PORTDOCS%%@dirrm share/doc/gp