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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-08-23 17:28:41 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-08-23 17:28:41 +0000 |
| commit | 2e559ca48c93b075905245367e11e30b9be34b2c (patch) | |
| tree | 3eace3d9838de2869de7f6b48a4b73389251db85 /biology | |
| parent | 615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3 (diff) | |
| download | ports-2e559ca48c93b075905245367e11e30b9be34b2c.tar.gz ports-2e559ca48c93b075905245367e11e30b9be34b2c.zip | |
biology/bfc: Correct sequencing errors from Illumina sequencing data
BFC is a standalone high-performance tool for correcting sequencing
errors from Illumina sequencing data. It is specifically designed for
high-coverage whole-genome human data, though also performs well for
small genomes.
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/bfc/Makefile | 20 | ||||
| -rw-r--r-- | biology/bfc/distinfo | 3 | ||||
| -rw-r--r-- | biology/bfc/files/patch-Makefile | 36 | ||||
| -rw-r--r-- | biology/bfc/files/patch-kthread.c | 10 | ||||
| -rw-r--r-- | biology/bfc/pkg-descr | 6 |
6 files changed, 76 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 24a2bc0890c3..b3a5731f8a6a 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -9,6 +9,7 @@ SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools + SUBDIR += bfc SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc diff --git a/biology/bfc/Makefile b/biology/bfc/Makefile new file mode 100644 index 000000000000..967e8829f16a --- /dev/null +++ b/biology/bfc/Makefile @@ -0,0 +1,20 @@ +PORTNAME= bfc +DISTVERSION= g20150417 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Correct sequencing errors from Illumina sequencing data + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/LICENSE.txt + +USES= gmake +USE_GITHUB= yes + +GH_ACCOUNT= lh3 +GH_TAGNAME= 69ab176e + +INSTALL_TARGET= install-strip +PLIST_FILES= bin/bfc bin/hash2cnt + +.include <bsd.port.mk> diff --git a/biology/bfc/distinfo b/biology/bfc/distinfo new file mode 100644 index 000000000000..b2e518d4e0c8 --- /dev/null +++ b/biology/bfc/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1629673065 +SHA256 (lh3-bfc-g20150417-69ab176e_GH0.tar.gz) = 202913e590421d23571c5e7c5cb9c23730ee57cb5b2eaa0e7806d33c49482452 +SIZE (lh3-bfc-g20150417-69ab176e_GH0.tar.gz) = 68138 diff --git a/biology/bfc/files/patch-Makefile b/biology/bfc/files/patch-Makefile new file mode 100644 index 000000000000..b031139aa596 --- /dev/null +++ b/biology/bfc/files/patch-Makefile @@ -0,0 +1,36 @@ +--- Makefile.orig 2015-04-17 05:17:58 UTC ++++ Makefile +@@ -1,11 +1,17 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once ++CC?= gcc ++# Allow env to set optimization and warning levels, then add required flags ++CFLAGS?= -g -Wall -O2 ++CFLAGS+= -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once + CPPFLAGS= + INCLUDES= + OBJS= kthread.o utils.o bseq.o bbf.o htab.o count.o correct.o bfc.o + PROG= bfc hash2cnt + LIBS= -lm -lz -lpthread + ++MKDIR?= mkdir ++INSTALL?= install ++STRIP?= strip ++ + .SUFFIXES:.c .o + + .c.o: +@@ -18,6 +24,13 @@ bfc:$(OBJS) + + hash2cnt:hash2cnt.o + $(CC) $(CFLAGS) $< -o $@ ++ ++install: ++ $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin ++ $(INSTALL) -c $(PROG) $(DESTDIR)$(PREFIX)/bin ++ ++install-strip: install ++ $(STRIP) $(DESTDIR)$(PREFIX)/bin/* + + clean: + rm -fr gmon.out *.o ext/*.o a.out $(PROG) *~ *.a *.dSYM session* diff --git a/biology/bfc/files/patch-kthread.c b/biology/bfc/files/patch-kthread.c new file mode 100644 index 000000000000..a019b17beea5 --- /dev/null +++ b/biology/bfc/files/patch-kthread.c @@ -0,0 +1,10 @@ +--- kthread.c.orig 2021-08-22 22:59:48 UTC ++++ kthread.c +@@ -1,6 +1,7 @@ + #include <pthread.h> + #include <stdlib.h> + #include <limits.h> ++#include <inttypes.h> + + /************ + * kt_for() * diff --git a/biology/bfc/pkg-descr b/biology/bfc/pkg-descr new file mode 100644 index 000000000000..a2135b6a4ecc --- /dev/null +++ b/biology/bfc/pkg-descr @@ -0,0 +1,6 @@ +BFC is a standalone high-performance tool for correcting sequencing +errors from Illumina sequencing data. It is specifically designed for +high-coverage whole-genome human data, though also performs well for +small genomes. + +WWW: https://github.com/lh3/bfc |