From 627a60b50dc1c956cefd5a72872ace30ef1c70b6 Mon Sep 17 00:00:00 2001 From: jschauma Date: Fri, 26 Sep 2003 03:29:59 +0000 Subject: 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. --- 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(+) create mode 100644 biology/gp/DESCR create mode 100644 biology/gp/Makefile create mode 100644 biology/gp/PLIST create mode 100644 biology/gp/README.html create mode 100644 biology/gp/distinfo create mode 100644 biology/gp/patches/patch-aa create mode 100644 biology/gp/patches/patch-ab (limited to 'biology') diff --git a/biology/gp/DESCR b/biology/gp/DESCR new file mode 100644 index 00000000000..0c7ef2fc23a --- /dev/null +++ b/biology/gp/DESCR @@ -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 --git a/biology/gp/Makefile b/biology/gp/Makefile new file mode 100644 index 00000000000..d9e5c08b086 --- /dev/null +++ b/biology/gp/Makefile @@ -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 +HOMEPAGE= http://www.bioinformatics.org/genpak/ +COMMENT= Manipulate DNA/RNA sequence in a Unix fashion + +USE_BUILDLINK2= YES + +.include "../../mk/bsd.pkg.mk" diff --git a/biology/gp/PLIST b/biology/gp/PLIST new file mode 100644 index 00000000000..f4b93eb1c8f --- /dev/null +++ b/biology/gp/PLIST @@ -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 --git a/biology/gp/README.html b/biology/gp/README.html new file mode 100644 index 00000000000..003a4dc1a03 --- /dev/null +++ b/biology/gp/README.html @@ -0,0 +1,95 @@ + + + + +The NetBSD Packages Collection: local.biology/gp + + + + +

+ +

The NetBSD Packages Collection: local.biology/gp

+ +

Brief description of the package:
+ +Manipulate DNA/RNA sequence in a Unix fashion + +

+ +

Please read the file "DESCR" for a +longer description, or browse the package's +history. +

+ +

This package has a home page at http://www.bioinformatics.org/genpak.

+ + + +

The package is located in the +"local.biology/gp" +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 +top of the packages tree. +

+ +

Problem reports, updates or suggestions for this package should be +reported with +send-pr.

+ +

+The following security vulnerabilities are known for local.biology/gp +at May 29 06:00 + +: +

(no vulnerabilities known)

+If you have a vulnerable package installed on any machine, you are +advised to remove the package +immediately, using the standard package tools. +The audit-packages +package locates any installed package which has been mentioned in security +advisories as being vulnerable. +

+ + +

+This package requires the following package(s) to build: +none +. +

+This package requires the following package(s) to run: +none +. +

+ +

+Select one of the links below to download the +package in precompiled binary form for installation with pkg_add(1). +Available machine architectures and package versions: + + +
+ +

+The NetBSD packages collection is designed to permit + easy installation from source - + particularly useful if the latest binary package is + not available for your chosen platform. +

+ +

+[ + Go up one level +| + Go to top of packages tree +| + List all packages +] + + diff --git a/biology/gp/distinfo b/biology/gp/distinfo new file mode 100644 index 00000000000..193686b86b7 --- /dev/null +++ b/biology/gp/distinfo @@ -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 --git a/biology/gp/patches/patch-aa b/biology/gp/patches/patch-aa new file mode 100644 index 00000000000..3544d8ba74f --- /dev/null +++ b/biology/gp/patches/patch-aa @@ -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=$(TREE)/share/examples + + # documentation. + # If you want to install documents automagically, type: diff --git a/biology/gp/patches/patch-ab b/biology/gp/patches/patch-ab new file mode 100644 index 00000000000..d45c803973f --- /dev/null +++ b/biology/gp/patches/patch-ab @@ -0,0 +1,21 @@ +$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) + -- cgit v1.2.3