From 164e1138b86d9d5bf75a6047a99fa1e3ea9838e1 Mon Sep 17 00:00:00 2001 From: Ruslan Makhmatkhanov Date: Fri, 25 Sep 2015 18:39:36 +0000 Subject: 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 --- biology/Makefile | 1 + biology/bwa/Makefile | 28 ++++++++++++++++++++++++++++ biology/bwa/distinfo | 2 ++ biology/bwa/files/patch-Makefile | 11 +++++++++++ biology/bwa/files/patch-bwt_lite.c | 11 +++++++++++ biology/bwa/files/patch-bwtgap.c | 11 +++++++++++ biology/bwa/files/patch-bwtgap.h | 15 +++++++++++++++ biology/bwa/pkg-descr | 5 +++++ 8 files changed, 84 insertions(+) create mode 100644 biology/bwa/Makefile create mode 100644 biology/bwa/distinfo create mode 100644 biology/bwa/files/patch-Makefile create mode 100644 biology/bwa/files/patch-bwt_lite.c create mode 100644 biology/bwa/files/patch-bwtgap.c create mode 100644 biology/bwa/files/patch-bwtgap.h create mode 100644 biology/bwa/pkg-descr diff --git a/biology/Makefile b/biology/Makefile index 34ca709f62d2..8ded92f1a10c 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -11,6 +11,7 @@ SUBDIR += biococoa SUBDIR += biojava SUBDIR += blat + SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq diff --git a/biology/bwa/Makefile b/biology/bwa/Makefile new file mode 100644 index 000000000000..c2678e0f6c76 --- /dev/null +++ b/biology/bwa/Makefile @@ -0,0 +1,28 @@ +# Created by: Jason Bacon +# $FreeBSD$ + +PORTNAME= bwa +PORTVERSION= 0.7.9a +CATEGORIES= biology +MASTER_SITES= SF/bio-bwa/ + +MAINTAINER= jwbacon@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 diff --git a/biology/bwa/distinfo b/biology/bwa/distinfo new file mode 100644 index 000000000000..70c5bb90053e --- /dev/null +++ b/biology/bwa/distinfo @@ -0,0 +1,2 @@ +SHA256 (bwa-0.7.9a.tar.bz2) = f5ad30e4e5ea86a8dcd6febcb6f620a75c82b03024f64a572017c295a962eadc +SIZE (bwa-0.7.9a.tar.bz2) = 166193 diff --git a/biology/bwa/files/patch-Makefile b/biology/bwa/files/patch-Makefile new file mode 100644 index 000000000000..e7d704d5e0b3 --- /dev/null +++ b/biology/bwa/files/patch-Makefile @@ -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) diff --git a/biology/bwa/files/patch-bwt_lite.c b/biology/bwa/files/patch-bwt_lite.c new file mode 100644 index 000000000000..e5059bc744a9 --- /dev/null +++ b/biology/bwa/files/patch-bwt_lite.c @@ -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; diff --git a/biology/bwa/files/patch-bwtgap.c b/biology/bwa/files/patch-bwtgap.c new file mode 100644 index 000000000000..2ede8889940b --- /dev/null +++ b/biology/bwa/files/patch-bwtgap.c @@ -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; diff --git a/biology/bwa/files/patch-bwtgap.h b/biology/bwa/files/patch-bwtgap.h new file mode 100644 index 000000000000..f00ed0f7509f --- /dev/null +++ b/biology/bwa/files/patch-bwtgap.h @@ -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; diff --git a/biology/bwa/pkg-descr b/biology/bwa/pkg-descr new file mode 100644 index 000000000000..2e40ad084670 --- /dev/null +++ b/biology/bwa/pkg-descr @@ -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/ -- cgit v1.2.3