From owner-dev-commits-ports-all@freebsd.org Mon Aug 23 17:27:47 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 8007066E9B0; Mon, 23 Aug 2021 17:27:47 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4GtfMR37Dhz4VYy; Mon, 23 Aug 2021 17:27:47 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 5372017D7E; Mon, 23 Aug 2021 17:27:47 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 17NHRlpa012626; Mon, 23 Aug 2021 17:27:47 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 17NHRlLD012625; Mon, 23 Aug 2021 17:27:47 GMT (envelope-from git) Date: Mon, 23 Aug 2021 17:27:47 GMT Message-Id: <202108231727.17NHRlLD012625@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 615c521bb3a0 - main - biology/flash: Fast Length Adjustment of SHort reads MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 23 Aug 2021 17:27:47 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3 commit 615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3 Author: Jason W. Bacon AuthorDate: 2021-08-23 17:26:47 +0000 Commit: Jason W. Bacon 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 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/