diff options
| author | Edwin Groothuis <edwin@FreeBSD.org> | 2008-05-24 07:03:23 +0000 |
|---|---|---|
| committer | Edwin Groothuis <edwin@FreeBSD.org> | 2008-05-24 07:03:23 +0000 |
| commit | c65af41a3b0e8a047f8159fa8fbd0bc8473e69e4 (patch) | |
| tree | 99d49f7c902d40dcdc3ac51ce6c1063b60097625 | |
| parent | New port: biology/consed viewing and editing workbench for sequence (diff) | |
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>
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/phd2fasta/distinfo | 3 | ||||
| -rw-r--r-- | biology/phd2fasta/files/patch-Makefile | 10 | ||||
| -rw-r--r-- | biology/phd2fasta/pkg-descr | 8 |
4 files changed, 22 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index a5d67b95304e..cca7466654dc 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -65,6 +65,7 @@ SUBDIR += p5-bioperl-run-devel SUBDIR += paml SUBDIR += phd2fasta + SUBDIR += phrap SUBDIR += phylip SUBDIR += platon SUBDIR += povchem diff --git a/biology/phd2fasta/distinfo b/biology/phd2fasta/distinfo new file mode 100644 index 000000000000..58ba11c427ee --- /dev/null +++ b/biology/phd2fasta/distinfo @@ -0,0 +1,3 @@ +MD5 (phd2fasta-acd-dist.tar.Z) = d72a5b20925d45ca87b353e20f3c673c +SHA256 (phd2fasta-acd-dist.tar.Z) = e73e190a9721e8f459e8589bd448114cf670054240439dec2c8cde8d9f97c6a0 +SIZE (phd2fasta-acd-dist.tar.Z) = 58431 diff --git a/biology/phd2fasta/files/patch-Makefile b/biology/phd2fasta/files/patch-Makefile new file mode 100644 index 000000000000..3dd2d7f8d370 --- /dev/null +++ b/biology/phd2fasta/files/patch-Makefile @@ -0,0 +1,10 @@ +--- Makefile.orig 2002-08-09 05:30:48.000000000 +0900 ++++ Makefile 2007-12-06 19:02:31.000000000 +0900 +@@ -1,5 +1,5 @@ +-CC=cc +-CFLAGS=-O -w ++CC?=cc ++CFLAGS+=-w + CLIB=-lm + + OBJ= phd2fasta.o \ diff --git a/biology/phd2fasta/pkg-descr b/biology/phd2fasta/pkg-descr new file mode 100644 index 000000000000..e965d0987bd0 --- /dev/null +++ b/biology/phd2fasta/pkg-descr @@ -0,0 +1,8 @@ +Phred and consed write sequence and quality value information in +'phd' output files. A phd file contains information in a header, +the called bases, the base quality values, and the base call trace +locations. Phd2fasta reads phd files and writes sequence and quality +value FASTA files, which phrap and cross_match need as input. +(Consed needs phd files in order to obtain the base call locations.) + +WWW: http://www.phrap.org/phredphrapconsed.html |