diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/gp/Makefile | 36 | ||||
| -rw-r--r-- | biology/gp/distinfo | 1 | ||||
| -rw-r--r-- | biology/gp/files/patch-Makefile | 51 | ||||
| -rw-r--r-- | biology/gp/files/patch-src::Makefile | 10 | ||||
| -rw-r--r-- | biology/gp/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/gp/pkg-descr | 9 | ||||
| -rw-r--r-- | biology/gp/pkg-plist | 54 |
8 files changed, 0 insertions, 163 deletions
diff --git a/biology/Makefile b/biology/Makefile index 52ca8f84d005..880d5e36e467 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -11,7 +11,6 @@ SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += gaussian98 - SUBDIR += gp SUBDIR += gperiodic SUBDIR += hmmer SUBDIR += kinemage diff --git a/biology/gp/Makefile b/biology/gp/Makefile deleted file mode 100644 index 088119d8fec1..000000000000 --- a/biology/gp/Makefile +++ /dev/null @@ -1,36 +0,0 @@ -# ex:ts=8 -# New ports collection makefile for: gp -# Date created: Feb 28, 2001 -# Whom: Ying-Chieh Liao <ijliao@FreeBSD.org> -# -# $FreeBSD$ -# - -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" ${WRKSRC}/Makefile - -.include <bsd.port.mk> diff --git a/biology/gp/distinfo b/biology/gp/distinfo deleted file mode 100644 index 1d640501a87b..000000000000 --- a/biology/gp/distinfo +++ /dev/null @@ -1 +0,0 @@ -MD5 (gp-0.25.tgz) = 35bc282e2da3d5af24cf44ed01a04551 diff --git a/biology/gp/files/patch-Makefile b/biology/gp/files/patch-Makefile deleted file mode 100644 index db0ffe3ad507..000000000000 --- a/biology/gp/files/patch-Makefile +++ /dev/null @@ -1,51 +0,0 @@ ---- Makefile.orig Tue Feb 13 22:41:12 2001 -+++ Makefile Wed Feb 28 01:01:15 2001 -@@ -5,15 +5,13 @@ - ###################################################################### - # Change the following to suit your needs - --SHELL=/bin/bash -- - # The directory root of your installation - # If you make a personal installation, change it to your home directory - # Default: /usr - # uncomment the following line to install to the default directories... - # TREE=/usr - # ...or the following line to install into your home directory: --TREE=$(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 deleted file mode 100644 index 345fb413bb5b..000000000000 --- a/biology/gp/files/patch-src::Makefile +++ /dev/null @@ -1,10 +0,0 @@ ---- 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 deleted file mode 100644 index c8710a783594..000000000000 --- a/biology/gp/pkg-comment +++ /dev/null @@ -1 +0,0 @@ -GP is a set of small utilities to manipulate DNA sequences diff --git a/biology/gp/pkg-descr b/biology/gp/pkg-descr deleted file mode 100644 index a8f362329a99..000000000000 --- a/biology/gp/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -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 deleted file mode 100644 index 07c9bb039bf9..000000000000 --- a/biology/gp/pkg-plist +++ /dev/null @@ -1,54 +0,0 @@ -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 |