From c65af41a3b0e8a047f8159fa8fbd0bc8473e69e4 Mon Sep 17 00:00:00 2001 From: Edwin Groothuis Date: Sat, 24 May 2008 07:03:23 +0000 Subject: 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 --- biology/phd2fasta/distinfo | 3 +++ biology/phd2fasta/files/patch-Makefile | 10 ++++++++++ biology/phd2fasta/pkg-descr | 8 ++++++++ 3 files changed, 21 insertions(+) create mode 100644 biology/phd2fasta/distinfo create mode 100644 biology/phd2fasta/files/patch-Makefile create mode 100644 biology/phd2fasta/pkg-descr (limited to 'biology/phd2fasta') 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 -- cgit v1.2.3