Date: Mon, 23 Aug 2021 17:27:47 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 615c521bb3a0 - main - biology/flash: Fast Length Adjustment of SHort reads Message-ID: <202108231727.17NHRlLD012625@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3 commit 615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-08-23 17:26:47 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-08-23 17:26:47 +0000 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. --- biology/Makefile | 1 + biology/flash/Makefile | 19 +++++++++++++++++++ biology/flash/distinfo | 3 +++ biology/flash/files/patch-Makefile | 25 +++++++++++++++++++++++++ biology/flash/pkg-descr | 9 +++++++++ 5 files changed, 57 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index 081fb65708b1..24a2bc0890c3 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -45,6 +45,7 @@ SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree + SUBDIR += flash SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic 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/
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