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| author | nbm <nbm@FreeBSD.org> | 2000-07-27 22:33:00 +0800 |
|---|---|---|
| committer | nbm <nbm@FreeBSD.org> | 2000-07-27 22:33:00 +0800 |
| commit | 32f1737c36b2ffa8feb90ba7a68579d37f3afc2e (patch) | |
| tree | de71cd8c9c636ef905a3ea56e87610e9e31a41c5 | |
| parent | f2358940cee1f1b3291aadb9b4a01ecb7d539600 (diff) | |
| download | freebsd-ports-gnome-32f1737c36b2ffa8feb90ba7a68579d37f3afc2e.tar.gz freebsd-ports-gnome-32f1737c36b2ffa8feb90ba7a68579d37f3afc2e.tar.zst freebsd-ports-gnome-32f1737c36b2ffa8feb90ba7a68579d37f3afc2e.zip | |
Add sim4, an implementation of the sim4 algorithm for aligning expressed
DNA with genomic sequences
PR: ports/20219
Submitted by: Johann Visagie <johann@egenetics.com>
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/sim4/Makefile | 23 | ||||
| -rw-r--r-- | biology/sim4/distinfo | 1 | ||||
| -rw-r--r-- | biology/sim4/files/patch-aa | 10 | ||||
| -rw-r--r-- | biology/sim4/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/sim4/pkg-descr | 11 | ||||
| -rw-r--r-- | biology/sim4/pkg-plist | 1 |
7 files changed, 48 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index f0b43f8b45c3..d91b479913aa 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -18,6 +18,7 @@ SUBDIR += psi88 SUBDIR += rasmol SUBDIR += seaview + SUBDIR += sim4 SUBDIR += tinker SUBDIR += xdrawchem SUBDIR += xmolwt diff --git a/biology/sim4/Makefile b/biology/sim4/Makefile new file mode 100644 index 000000000000..a988b24558ab --- /dev/null +++ b/biology/sim4/Makefile @@ -0,0 +1,23 @@ +# New ports collection makefile for: sim4 +# Date created: 27 July 2000 +# Whom: Johann Visagie <johann@egenetics.com> +# +# $FreeBSD$ +# + +PORTNAME= sim4 +PORTVERSION= 2000.07.13 +CATEGORIES= biology +MASTER_SITES= http://globin.cse.psu.edu/ftp/dist/sim4/ +DISTNAME= sim4 + +MAINTAINER= johann@egenetics.com + +WRKSRC= ${WRKDIR}/sim4.2000-07-13 + +ALL_TARGET= sim4 + +do-install: + @ ${INSTALL_PROGRAM} ${WRKSRC}/sim4 ${PREFIX}/bin + +.include <bsd.port.mk> diff --git a/biology/sim4/distinfo b/biology/sim4/distinfo new file mode 100644 index 000000000000..ac470bbbaf67 --- /dev/null +++ b/biology/sim4/distinfo @@ -0,0 +1 @@ +MD5 (sim4.tar.gz) = aad9ecab4978424fb6ec6cd60140f948 diff --git a/biology/sim4/files/patch-aa b/biology/sim4/files/patch-aa new file mode 100644 index 000000000000..83a5316370e9 --- /dev/null +++ b/biology/sim4/files/patch-aa @@ -0,0 +1,10 @@ +--- Makefile.orig Thu Jul 13 12:09:47 2000 ++++ Makefile Thu Jul 27 07:28:18 2000 +@@ -5,6 +5,6 @@ + # For gcc, ``-O2'' works well. + + sim4: +- cc -o sim4 -I. -O *.c -lm ++ ${CC} -o sim4 -I. ${CFLAGS} *.c -lm + clean: + rm -f sim4 *.o diff --git a/biology/sim4/pkg-comment b/biology/sim4/pkg-comment new file mode 100644 index 000000000000..7e50b5e0e13f --- /dev/null +++ b/biology/sim4/pkg-comment @@ -0,0 +1 @@ +An algorithm for aligning expressed DNA with genomic sequences diff --git a/biology/sim4/pkg-descr b/biology/sim4/pkg-descr new file mode 100644 index 000000000000..a5f4cdb174af --- /dev/null +++ b/biology/sim4/pkg-descr @@ -0,0 +1,11 @@ +This package implements the Sim4 algorithm for aligning expressed DNA +with genomic sequences, described in the paper: + +L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998) +"A computer program for aligning a cDNA sequence with a genomic DNA sequence." +Genome Research 8, 967-974. + +WWW: http://globin.cse.psu.edu/ + +- Johann +johann@egenetics.com diff --git a/biology/sim4/pkg-plist b/biology/sim4/pkg-plist new file mode 100644 index 000000000000..166054a68786 --- /dev/null +++ b/biology/sim4/pkg-plist @@ -0,0 +1 @@ +bin/sim4 |