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[pkgsrc/trunk]: pkgsrc/biology/gp Initial import of gp, one of the many packa...
details: https://anonhg.NetBSD.org/pkgsrc/rev/446259e243e8
branches: trunk
changeset: 462065:446259e243e8
user: jschauma <jschauma%pkgsrc.org@localhost>
date: Fri Sep 26 03:29:59 2003 +0000
description:
Initial import of gp, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.
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.
diffstat:
biology/gp/DESCR | 3 +
biology/gp/Makefile | 15 +++++++
biology/gp/PLIST | 50 +++++++++++++++++++++++
biology/gp/README.html | 95 +++++++++++++++++++++++++++++++++++++++++++++
biology/gp/distinfo | 6 ++
biology/gp/patches/patch-aa | 37 +++++++++++++++++
biology/gp/patches/patch-ab | 21 +++++++++
7 files changed, 227 insertions(+), 0 deletions(-)
diffs (255 lines):
diff -r 83af5ceedd15 -r 446259e243e8 biology/gp/DESCR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gp/DESCR Fri Sep 26 03:29:59 2003 +0000
@@ -0,0 +1,3 @@
+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.
diff -r 83af5ceedd15 -r 446259e243e8 biology/gp/Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gp/Makefile Fri Sep 26 03:29:59 2003 +0000
@@ -0,0 +1,15 @@
+# $NetBSD: Makefile,v 1.1.1.1 2003/09/26 03:29:59 jschauma Exp $
+#
+
+DISTNAME= gp-0.26
+CATEGORIES= biology
+MASTER_SITES= http://www.bioinformatics.org/genpak/
+EXTRACT_SUFX= .tgz
+
+MAINTAINER= hdp%cs.nmsu.edu@localhost
+HOMEPAGE= http://www.bioinformatics.org/genpak/
+COMMENT= Manipulate DNA/RNA sequence in a Unix fashion
+
+USE_BUILDLINK2= YES
+
+.include "../../mk/bsd.pkg.mk"
diff -r 83af5ceedd15 -r 446259e243e8 biology/gp/PLIST
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gp/PLIST Fri Sep 26 03:29:59 2003 +0000
@@ -0,0 +1,50 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/26 03:30:00 jschauma Exp $
+bin/gp_acc
+bin/gp_adjust
+bin/gp_cdndev
+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
+man/man1/Genpak.1
+man/man1/gp_acc.1
+man/man1/gp_adjust.1
+man/man1/gp_cdndev.1
+man/man1/gp_cusage.1
+man/man1/gp_digest.1
+man/man1/gp_dimer.1
+man/man1/gp_findorf.1
+man/man1/gp_gc.1
+man/man1/gp_getseq.1
+man/man1/gp_matrix.1
+man/man1/gp_mkmtx.1
+man/man1/gp_pattern.1
+man/man1/gp_primer.1
+man/man1/gp_qs.1
+man/man1/gp_randseq.1
+man/man1/gp_seq2prot.1
+man/man1/gp_slen.1
+man/man1/gp_tm.1
+man/man1/gp_trimer.1
+share/examples/genpak/ecoli.mtx
+share/examples/genpak/enzyme.enz
+share/examples/genpak/mporfs.seq
+share/examples/genpak/myco.cdn
+share/examples/genpak/sample.seq
+share/examples/genpak/standard.cdn
+@dirrm share/examples/genpak
diff -r 83af5ceedd15 -r 446259e243e8 biology/gp/README.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gp/README.html Fri Sep 26 03:29:59 2003 +0000
@@ -0,0 +1,95 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<!-- $NetBSD: README.html,v 1.1.1.1 2003/09/26 03:30:00 jschauma Exp $ -->
+<html>
+<head>
+<title>The NetBSD Packages Collection: local.biology/gp</title>
+</head>
+<body bgcolor="#ffffff">
+
+<a href="http://www.mckusick.com/beastie/mainpage/copyright.html";>
+<img align="right" src="../../templates/pkg-daemon.gif" alt="Daemon Power"
+ width="147" height="121" border="0">
+</a>
+<h1>The NetBSD Packages Collection: <i>local.biology/gp</i></h1>
+
+<p>Brief description of the package:<br>
+<I>
+Manipulate DNA/RNA sequence in a Unix fashion
+</I>
+</p>
+
+<p>Please read the file "<a href="DESCR">DESCR</a>" for a
+longer description, or browse the package's
+<A HREF="http://cvsweb.netbsd.org/bsdweb.cgi/pkgsrc/local.biology/gp/";>history</A>.
+</p>
+
+<p>This package has a home page at <a HREF="http://www.bioinformatics.org/genpak";>http://www.bioinformatics.org/genpak</a>.</p>
+
+
+
+<p>The package is located in the
+"<A HREF=".">local.biology/gp</A>"
+directory.
+The current source version of the package is
+"gp-0.26".
+For a summary on how to use the package collection, go to the
+<a href="../../README.html">top of the packages tree</a>.
+</p>
+
+<p>Problem reports, updates or suggestions for this package should be
+reported with
+<a href="http://www.netbsd.org/Misc/send-pr.html";>send-pr.</a></p>
+
+<P>
+The following security vulnerabilities are known for local.biology/gp
+at May 29 06:00
+
+:
+<UL>
+<I>(no vulnerabilities known)</I>
+</UL>
+If you have a vulnerable package installed on any machine, you are
+advised to remove the package
+immediately, using the standard package tools.
+The <a href="../../security/audit-packages/README.html">audit-packages</a>
+package locates any installed package which has been mentioned in security
+advisories as being vulnerable.
+</P>
+
+
+<p>
+This package requires the following package(s) to build:
+<EM>none</EM>
+.
+</p>
+<p>
+This package requires the following package(s) to run:
+<EM>none</EM>
+.
+</p>
+
+<p>
+Select one of the links below to <FONT COLOR="red">download</FONT> the
+package in precompiled binary form for installation with pkg_add(1).
+Available machine architectures and package versions:
+<TABLE>
+
+</TABLE>
+
+<p>
+The NetBSD packages collection is designed to permit
+ easy <a href="../../README">installation from source</a> -
+ particularly useful if the latest binary package is
+ not available for your chosen platform.
+</p>
+
+<hr noshade>
+[
+<a href="../README.html"> Go up one level</a>
+|
+<a href="../../README.html"> Go to top of packages tree</a>
+|
+<a href="../../README-all.html"> List all packages</a>
+]
+</body>
+</html>
diff -r 83af5ceedd15 -r 446259e243e8 biology/gp/distinfo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gp/distinfo Fri Sep 26 03:29:59 2003 +0000
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1.1.1 2003/09/26 03:30:00 jschauma Exp $
+
+SHA1 (gp-0.26.tgz) = 18107463df9bb33d12cc0f0fc6a6f17985492666
+Size (gp-0.26.tgz) = 141159 bytes
+SHA1 (patch-aa) = 2c3078fe296c281162f5ea9bca7773cdbdda9577
+SHA1 (patch-ab) = ce6ec76011f18a9a86b8c65ba5541848e298e27a
diff -r 83af5ceedd15 -r 446259e243e8 biology/gp/patches/patch-aa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gp/patches/patch-aa Fri Sep 26 03:29:59 2003 +0000
@@ -0,0 +1,37 @@
+$NetBSD: patch-aa,v 1.1.1.1 2003/09/26 03:30:00 jschauma Exp $
+
+--- Makefile.orig Thu May 17 13:27:07 2001
++++ Makefile
+@@ -5,20 +5,20 @@
+ ######################################################################
+ # Change the following to suit your needs
+
+-SHELL=/bin/bash
++SHELL=${SH}
+
+ # The directory root of your installation
+ # If you make a personal installation, change it to your home directory
+ # Default: /usr
+ # uncomment the following line to install to the default directories...
+-TREE=/usr
++TREE=${PREFIX}
+ # ...or the following line to install into your home directory:
+ # TREE=$(HOME)
+
+ # if you don't have the gd graphic library installed, you have to comment out or
+ # delete the following line. However, gp_map is such a nice program, so you
+ # better go to www.boutell.com and download the gd library.
+-GDPROGRAMS=gp_map
++# GDPROGRAMS=gp_map
+
+ # Directory to install the programs themselves.
+ # Default: /usr/local/bin
+@@ -28,7 +28,7 @@ BINDIR=$(TREE)/bin
+ MANDIR=$(TREE)/man
+
+ #directory to install the data directory
+-DATADIR=$(TREE)/lib
++DATADIR=$(TREE)/share/examples
+
+ # documentation.
+ # If you want to install documents automagically, type:
diff -r 83af5ceedd15 -r 446259e243e8 biology/gp/patches/patch-ab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/gp/patches/patch-ab Fri Sep 26 03:29:59 2003 +0000
@@ -0,0 +1,21 @@
+$NetBSD: patch-ab,v 1.1.1.1 2003/09/26 03:30:00 jschauma Exp $
+
+--- src/Makefile.orig 2001-05-17 15:27:06.000000000 -0400
++++ src/Makefile 2003-09-25 23:22:01.000000000 -0400
+@@ -5,14 +5,13 @@
+ ######################################################################
+ # Change the following to suit your needs
+
+-SHELL=/bin/bash
+-CC=gcc
++SHELL=${SH}
+ LIBS= -lz -lm
+ #CFLAGS= -DNLS -DGZ
+
+ all: $(PROGRAMS) $(GPPROGRAMS)
+
+-$(PROGRAMS): gp%: gp%.o genpak.h genpak.o
++$(PROGRAMS): gp*: gp*.c genpak.h genpak.o
+ @echo Creating $@
+ $(CC) $(CFLAGS) -o $@ genpak.o $< $(LIBS)
+
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