diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2018-04-02 16:50:46 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2018-04-02 16:50:46 +0000 |
| commit | 69f9d7e451312560b4485ddfa75b4d3a63a448a4 (patch) | |
| tree | 25b7473f6ca60d44b3fbcf8cbc1bcf3045a84458 /biology/rainbow | |
| parent | ae3f123f18044a50fec073fc127b9a2e93e6ec4f (diff) | |
| download | ports-69f9d7e451312560b4485ddfa75b4d3a63a448a4.tar.gz ports-69f9d7e451312560b4485ddfa75b4d3a63a448a4.zip | |
biology/rainbow: Efficient clustering and assembling of short reads
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D14924
Notes
Notes:
svn path=/head/; revision=466235
Diffstat (limited to 'biology/rainbow')
| -rw-r--r-- | biology/rainbow/Makefile | 26 | ||||
| -rw-r--r-- | biology/rainbow/distinfo | 3 | ||||
| -rw-r--r-- | biology/rainbow/files/patch-Makefile | 10 | ||||
| -rw-r--r-- | biology/rainbow/pkg-descr | 10 |
4 files changed, 49 insertions, 0 deletions
diff --git a/biology/rainbow/Makefile b/biology/rainbow/Makefile new file mode 100644 index 000000000000..0fe16b14a1e8 --- /dev/null +++ b/biology/rainbow/Makefile @@ -0,0 +1,26 @@ +# $FreeBSD$ + +PORTNAME= rainbow +DISTVERSION= 2.0.4 +CATEGORIES= biology +MASTER_SITES= SF/bio-rainbow +DISTNAME= rainbow_${PORTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Efficient clustering and assembling of short reads, especially for RAD + +LICENSE= GPLv3+ + +USES= gmake + +PLIST_FILES= bin/rainbow bin/ezmsim bin/rbasm + +do-install: + @${MKDIR} ${STAGEDIR}${PREFIX}/bin + ${INSTALL_PROGRAM} \ + ${WRKSRC}/rainbow \ + ${WRKSRC}/ezmsim \ + ${WRKSRC}/rbasm \ + ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> diff --git a/biology/rainbow/distinfo b/biology/rainbow/distinfo new file mode 100644 index 000000000000..f58d4d136c56 --- /dev/null +++ b/biology/rainbow/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1520455667 +SHA256 (rainbow_2.0.4.tar.gz) = 79281aae3bccd1ad467afef6fc7c8327aaa8d56f538821e2833d2b8f26b5bafc +SIZE (rainbow_2.0.4.tar.gz) = 77111 diff --git a/biology/rainbow/files/patch-Makefile b/biology/rainbow/files/patch-Makefile new file mode 100644 index 000000000000..eb3f2af46dae --- /dev/null +++ b/biology/rainbow/files/patch-Makefile @@ -0,0 +1,10 @@ +--- Makefile.orig 2015-07-27 18:28:54 UTC ++++ Makefile +@@ -1,5 +1,5 @@ +-CC=gcc +-CFLAGS= -W -O2 -Wall -Wno-self-assign -Wno-unused-function ++CC?=gcc ++CFLAGS?= -W -O2 -Wall -Wno-self-assign -Wno-unused-function + DFLAGS= -D_FILE_OFFSET_BITS=64 + GLIBS=-lm + GENERIC_SRC= string.h bitvec.h file_reader.h hashset.h sort.h list.h dna.h heap.h stdaln.h vector.h diff --git a/biology/rainbow/pkg-descr b/biology/rainbow/pkg-descr new file mode 100644 index 000000000000..395ad106b586 --- /dev/null +++ b/biology/rainbow/pkg-descr @@ -0,0 +1,10 @@ +Rainbow provides an ultra-fast and memory-efficient solution to clustering and +assembling short genetic sequence reads produced by Restriction site Associated +DNA Sequencing (RAD-seq). It does this by, first, clustering reads using a +spaced seed method, then it divides potential groups into haplotypes in a +top-down manner. Next, along a guide tree, it iteratively merges sibling +leaves in a bottom-up manner if they are similar enough. Finally, Rainbow uses +a greedy algorithm to locally assemble merged reads into contigs. Both optimal +and suboptimal assembly results are output. + +WWW: http://sourceforge.net/projects/bio-rainbow/ |