git: 615c521bb3a0 - main - biology/flash: Fast Length Adjustment of SHort reads

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3

commit 615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-08-23 17:26:47 +0000
Commit:     Jason W. Bacon <jwb at 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 at 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/