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| author | jwb <jwb@FreeBSD.org> | 2018-04-04 04:57:05 +0800 |
|---|---|---|
| committer | jwb <jwb@FreeBSD.org> | 2018-04-04 04:57:05 +0800 |
| commit | 79e55e9a65db3bc66b6460f11b1e6d7beeae3fc6 (patch) | |
| tree | a0d508175a8de3b02706eee236b6988159598b6b /biology | |
| parent | 584e40cc6c255dc6e69862cc9e0b87ff15457d3b (diff) | |
| download | freebsd-ports-gnome-79e55e9a65db3bc66b6460f11b1e6d7beeae3fc6.tar.gz freebsd-ports-gnome-79e55e9a65db3bc66b6460f11b1e6d7beeae3fc6.tar.zst freebsd-ports-gnome-79e55e9a65db3bc66b6460f11b1e6d7beeae3fc6.zip | |
biology/seqtk: Tool for processing sequences in FASTA/FASTQ format
Approved by: jrm
Differential Revision: https://reviews.freebsd.org/D14954
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/seqtk/Makefile | 21 | ||||
| -rw-r--r-- | biology/seqtk/distinfo | 3 | ||||
| -rw-r--r-- | biology/seqtk/files/patch-Makefile | 20 | ||||
| -rw-r--r-- | biology/seqtk/pkg-descr | 6 |
5 files changed, 51 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 9ece6c0a691f..5c013b34401b 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -106,6 +106,7 @@ SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio + SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust diff --git a/biology/seqtk/Makefile b/biology/seqtk/Makefile new file mode 100644 index 000000000000..b625d561742f --- /dev/null +++ b/biology/seqtk/Makefile @@ -0,0 +1,21 @@ +# $FreeBSD$ + +PORTNAME= seqtk +DISTVERSION= 1.2-8 +DISTVERSIONSUFFIX= -gd210c57 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Tool for processing sequences in FASTA/FASTQ format + +LICENSE= GPLv2 + +USE_GITHUB= yes +GH_ACCOUNT= lh3 + +PLIST_FILES= bin/seqtk + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/seqtk ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> diff --git a/biology/seqtk/distinfo b/biology/seqtk/distinfo new file mode 100644 index 000000000000..430869c941bf --- /dev/null +++ b/biology/seqtk/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1522780777 +SHA256 (lh3-seqtk-1.2-8-gd210c57_GH0.tar.gz) = 557317aab7f8cc306a98cd1148449f1e2edd7cd7c78ad5254ba955dfee518fa0 +SIZE (lh3-seqtk-1.2-8-gd210c57_GH0.tar.gz) = 21166 diff --git a/biology/seqtk/files/patch-Makefile b/biology/seqtk/files/patch-Makefile new file mode 100644 index 000000000000..6d8f5ee8535d --- /dev/null +++ b/biology/seqtk/files/patch-Makefile @@ -0,0 +1,20 @@ +--- Makefile.orig 2017-11-07 19:42:14 UTC ++++ Makefile +@@ -1,10 +1,11 @@ +-CC=gcc +-CFLAGS=-g -Wall -O2 -Wno-unused-function ++CC ?= gcc ++CFLAGS ?= -g -Wall -O2 -Wno-unused-function ++LDFLAGS += -lz -lm + +-all:seqtk ++all: seqtk + +-seqtk:seqtk.c khash.h kseq.h +- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm ++seqtk: seqtk.c khash.h kseq.h ++ $(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS) + + clean: +- rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* ++ rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* diff --git a/biology/seqtk/pkg-descr b/biology/seqtk/pkg-descr new file mode 100644 index 000000000000..4cc42a9b9b87 --- /dev/null +++ b/biology/seqtk/pkg-descr @@ -0,0 +1,6 @@ +Seqtk is a fast and lightweight tool for processing sequences in the FASTA or +FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be +optionally compressed by gzip. It performs basic file conversions and edits +much like standard Unix tools do with text files. + +WWW: https://github.com/lh3/seqtk |