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| author | edwin <edwin@FreeBSD.org> | 2008-05-24 15:01:56 +0800 |
|---|---|---|
| committer | edwin <edwin@FreeBSD.org> | 2008-05-24 15:01:56 +0800 |
| commit | e64901a3ca2ac457d0a60e98c796227899c750e3 (patch) | |
| tree | 871a882cdc20ee06be99c2cc8f0831c8e3be2c98 /biology | |
| parent | 8f4cd660b1578b7ac6d555650ab5599eb5e0e4a6 (diff) | |
| download | freebsd-ports-gnome-e64901a3ca2ac457d0a60e98c796227899c750e3.tar.gz freebsd-ports-gnome-e64901a3ca2ac457d0a60e98c796227899c750e3.tar.zst freebsd-ports-gnome-e64901a3ca2ac457d0a60e98c796227899c750e3.zip | |
New port: biology/consed viewing and editing workbench for sequence
assembly
Consed is a tool for viewing, editing, and finishing sequence
assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/phd2fasta/Makefile | 48 |
2 files changed, 49 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 3c4484cea3a9..a5d67b95304e 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -64,6 +64,7 @@ SUBDIR += p5-bioperl-run SUBDIR += p5-bioperl-run-devel SUBDIR += paml + SUBDIR += phd2fasta SUBDIR += phylip SUBDIR += platon SUBDIR += povchem diff --git a/biology/phd2fasta/Makefile b/biology/phd2fasta/Makefile new file mode 100644 index 000000000000..ef0df20fa7dc --- /dev/null +++ b/biology/phd2fasta/Makefile @@ -0,0 +1,48 @@ +# New ports collection makefile for: phd2fasta +# Date created: 6 December 2007 +# Whom: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> +# +# $FreeBSD$ +# + +PORTNAME= phd2fasta +PORTVERSION= 0.990622.f +CATEGORIES= biology +MASTER_SITES= # put the tarball manually +DISTFILES= phd2fasta-acd-dist.tar.Z + +MAINTAINER= mzaki@biol.s.u-tokyo.ac.jp +COMMENT= A converter from output files of Phred/Consed to FASTA files + +RESTRICTED= Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use. + +NO_WRKSUBDIR= yes + +ALL_TARGET= phd2fasta + +BINMODE= 0111 # avoid copying binaries as required by the agreement +BINARIES= phd2fasta +PLIST_FILES= bin/phd2fasta + +PORTDOCS= PHD2FASTA.DOC + +.include <bsd.port.pre.mk> + +.for f in ${DISTFILES} +.if !exists(${DISTDIR}/${f}) +IGNORE= you must request the source code \(${f}\) via e-mail, place it manually in ${DISTDIR}, and then try it again +.endif +.endfor + +do-install: +.for f in ${BINARIES} + @${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin/ +.endfor +.if !defined(NOPORTDOCS) + @${MKDIR} ${DOCSDIR} +.for f in ${PORTDOCS} + @${INSTALL_DATA} ${WRKSRC}/${f} ${DOCSDIR} +.endfor +.endif + +.include <bsd.port.post.mk> |