svn commit: r397851 - in head/biology: . bwa bwa/files
Ruslan Makhmatkhanov
rm at FreeBSD.org
Fri Sep 25 18:39:40 UTC 2015
Author: rm
Date: Fri Sep 25 18:39:36 2015
New Revision: 397851
URL: https://svnweb.freebsd.org/changeset/ports/397851
Log:
BWA is a program for aligning sequencing reads against a large reference
genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.
WWW: http://sourceforge.net/projects/bio-bwa/
PR: 203158
Submitted by: Jason Bacon <jwbacon at tds.net>
Added:
head/biology/bwa/
head/biology/bwa/Makefile (contents, props changed)
head/biology/bwa/distinfo (contents, props changed)
head/biology/bwa/files/
head/biology/bwa/files/patch-Makefile (contents, props changed)
head/biology/bwa/files/patch-bwt_lite.c (contents, props changed)
head/biology/bwa/files/patch-bwtgap.c (contents, props changed)
head/biology/bwa/files/patch-bwtgap.h (contents, props changed)
head/biology/bwa/pkg-descr (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Fri Sep 25 18:37:24 2015 (r397850)
+++ head/biology/Makefile Fri Sep 25 18:39:36 2015 (r397851)
@@ -11,6 +11,7 @@
SUBDIR += biococoa
SUBDIR += biojava
SUBDIR += blat
+ SUBDIR += bwa
SUBDIR += cd-hit
SUBDIR += cdbfasta
SUBDIR += chemeq
Added: head/biology/bwa/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bwa/Makefile Fri Sep 25 18:39:36 2015 (r397851)
@@ -0,0 +1,28 @@
+# Created by: Jason Bacon <jwbacon at tds.net>
+# $FreeBSD$
+
+PORTNAME= bwa
+PORTVERSION= 0.7.9a
+CATEGORIES= biology
+MASTER_SITES= SF/bio-bwa/
+
+MAINTAINER= jwbacon at tds.net
+COMMENT= Burrows-Wheeler sequence aligner
+
+LICENSE= GPLv3
+
+USES= perl5 shebangfix tar:bzip2
+SHEBANG_FILES= qualfa2fq.pl xa2multi.pl
+USE_PERL5= run
+
+PLIST_FILES= bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl man/man1/bwa.1.gz
+
+# Avoid #error in emmintrin.h
+CFLAGS+= -msse2
+
+do-install:
+ ${INSTALL_PROGRAM} ${WRKSRC}/bwa ${STAGEDIR}${PREFIX}/bin
+ ${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${STAGEDIR}${PREFIX}/bin
+ ${INSTALL_MAN} ${WRKSRC}/*.1 ${STAGEDIR}${MAN1PREFIX}/man/man1
+
+.include <bsd.port.mk>
Added: head/biology/bwa/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bwa/distinfo Fri Sep 25 18:39:36 2015 (r397851)
@@ -0,0 +1,2 @@
+SHA256 (bwa-0.7.9a.tar.bz2) = f5ad30e4e5ea86a8dcd6febcb6f620a75c82b03024f64a572017c295a962eadc
+SIZE (bwa-0.7.9a.tar.bz2) = 166193
Added: head/biology/bwa/files/patch-Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bwa/files/patch-Makefile Fri Sep 25 18:39:36 2015 (r397851)
@@ -0,0 +1,11 @@
+--- Makefile.orig 2014-05-19 13:11:41 UTC
++++ Makefile
+@@ -1,6 +1,6 @@
+-CC= gcc
++CC?= gcc
+ #CC= clang --analyze
+-CFLAGS= -g -Wall -Wno-unused-function -O2
++CFLAGS?= -g -Wall -Wno-unused-function -O2
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+ AR= ar
+ DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
Added: head/biology/bwa/files/patch-bwt_lite.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bwa/files/patch-bwt_lite.c Fri Sep 25 18:39:36 2015 (r397851)
@@ -0,0 +1,11 @@
+--- bwt_lite.c.orig 2014-05-19 13:11:41 UTC
++++ bwt_lite.c
+@@ -48,7 +48,7 @@ bwtl_t *bwtl_seq2bwtl(int len, const uin
+ }
+ { // generate cnt_table
+ for (i = 0; i != 256; ++i) {
+- u_int32_t j, x = 0;
++ uint32_t j, x = 0;
+ for (j = 0; j != 4; ++j)
+ x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
+ b->cnt_table[i] = x;
Added: head/biology/bwa/files/patch-bwtgap.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bwa/files/patch-bwtgap.c Fri Sep 25 18:39:36 2015 (r397851)
@@ -0,0 +1,11 @@
+--- bwtgap.c.orig 2014-02-25 21:20:01 UTC
++++ bwtgap.c
+@@ -58,7 +58,7 @@ static inline void gap_push(gap_stack_t
+ q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries);
+ }
+ p = q->stack + q->n_entries;
+- p->info = (u_int32_t)score<<21 | i; p->k = k; p->l = l;
++ p->info = (uint32_t)score<<21 | i; p->k = k; p->l = l;
+ p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape;
+ p->n_ins = n_ins; p->n_del = n_del;
+ p->state = state;
Added: head/biology/bwa/files/patch-bwtgap.h
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bwa/files/patch-bwtgap.h Fri Sep 25 18:39:36 2015 (r397851)
@@ -0,0 +1,15 @@
+--- bwtgap.h.orig 2014-02-25 21:20:01 UTC
++++ bwtgap.h
+@@ -5,9 +5,9 @@
+ #include "bwtaln.h"
+
+ typedef struct { // recursion stack
+- u_int32_t info; // score<<21 | i
+- u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
+- u_int32_t n_ins:16, n_del:16;
++ uint32_t info; // score<<21 | i
++ uint32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
++ uint32_t n_ins:16, n_del:16;
+ int last_diff_pos;
+ bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
+ } gap_entry_t;
Added: head/biology/bwa/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bwa/pkg-descr Fri Sep 25 18:39:36 2015 (r397851)
@@ -0,0 +1,5 @@
+BWA is a program for aligning sequencing reads against a large reference
+genome (e.g. human genome). It has two major components, one for read shorter
+than 150bp and the other for longer reads.
+
+WWW: http://sourceforge.net/projects/bio-bwa/
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