diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-08-23 12:26:47 -0500 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-08-23 12:26:47 -0500 |
| commit | 615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3 (patch) | |
| tree | 3a3b74f44b202170697232cab268c173a989cb9a /biology/flash | |
| parent | devel/capnproto: upgrade to 0.9.0 (diff) | |
biology/flash: Fast Length Adjustment of SHort reads
FLASH (Fast Length Adjustment of SHort reads) is a very fast and
accurate software tool to merge paired-end reads from next-generation
sequencing experiments. FLASH is designed to merge pairs of reads when
the original DNA fragments are shorter than twice the length of reads.
The resulting longer reads can significantly improve genome assemblies.
They can also improve transcriptome assembly when FLASH is used to
merge RNA-seq data.
Diffstat (limited to 'biology/flash')
| -rw-r--r-- | biology/flash/Makefile | 19 | ||||
| -rw-r--r-- | biology/flash/distinfo | 3 | ||||
| -rw-r--r-- | biology/flash/files/patch-Makefile | 25 | ||||
| -rw-r--r-- | biology/flash/pkg-descr | 9 |
4 files changed, 56 insertions, 0 deletions
diff --git a/biology/flash/Makefile b/biology/flash/Makefile new file mode 100644 index 000000000000..82af7793197b --- /dev/null +++ b/biology/flash/Makefile @@ -0,0 +1,19 @@ +PORTNAME= flash +DISTVERSION= 1.2.11 +CATEGORIES= biology +MASTER_SITES= http://ccb.jhu.edu/software/FLASH/ +DISTNAME= FLASH-${DISTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Fast Length Adjustment of SHort reads + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +USES= gmake + +ALL_TARGET= flash + +PLIST_FILES= bin/flash + +.include <bsd.port.mk> diff --git a/biology/flash/distinfo b/biology/flash/distinfo new file mode 100644 index 000000000000..5614e0143d98 --- /dev/null +++ b/biology/flash/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1629671970 +SHA256 (FLASH-1.2.11.tar.gz) = 685ca6f7fedda07434d8ee03c536f4763385671c4509c5bb48beb3055fd236ac +SIZE (FLASH-1.2.11.tar.gz) = 48889 diff --git a/biology/flash/files/patch-Makefile b/biology/flash/files/patch-Makefile new file mode 100644 index 000000000000..79852777bb6b --- /dev/null +++ b/biology/flash/files/patch-Makefile @@ -0,0 +1,25 @@ +--- Makefile.orig 2014-08-04 23:18:10 UTC ++++ Makefile +@@ -7,12 +7,21 @@ + # use a non-default compiler, extra preprocessor flags (e.g. to find headers), + # or extra linker flags (e.g. to find libraries). + +-CFLAGS += -O2 -Wall -std=c99 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 ++# Let env set optimization and warning level, then add required flags ++CFLAGS ?= -O2 -Wall ++CFLAGS += -std=c99 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 + LDLIBS := -lz -lpthread + OBJ := combine_reads.o flash.o iostream.o read_io.o read_queue.o read_util.o util.o + EXE := flash + ++MKDIR ?= mkdir ++INSTALL ?= install ++ + $(EXE):$(OBJ) ++ ++install: ++ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c flash ${DESTDIR}${PREFIX}/bin + + clean: + rm -f $(OBJ) $(EXE) diff --git a/biology/flash/pkg-descr b/biology/flash/pkg-descr new file mode 100644 index 000000000000..65b83f1d2db6 --- /dev/null +++ b/biology/flash/pkg-descr @@ -0,0 +1,9 @@ +FLASH (Fast Length Adjustment of SHort reads) is a very fast and +accurate software tool to merge paired-end reads from next-generation +sequencing experiments. FLASH is designed to merge pairs of reads when +the original DNA fragments are shorter than twice the length of reads. +The resulting longer reads can significantly improve genome assemblies. +They can also improve transcriptome assembly when FLASH is used to +merge RNA-seq data. + +WWW: http://ccb.jhu.edu/software/FLASH/ |