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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2018-04-03 18:23:54 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2018-04-03 18:23:54 +0000 |
| commit | 9db7a5f181c7b8e23660594e11a8b28c7d3319bd (patch) | |
| tree | 3741a1ffdad908f9216f1d015e1c47d29921643b /biology/trimadap | |
| parent | d46cfd0917265667bd40a1f17480f802e15b46d0 (diff) | |
| download | ports-9db7a5f181c7b8e23660594e11a8b28c7d3319bd.tar.gz ports-9db7a5f181c7b8e23660594e11a8b28c7d3319bd.zip | |
biology/trimadap: Trim adapter sequences from Illumina data
Reviewed by: mat
Approved by: jrm
Differential Revision: https://reviews.freebsd.org/D14935
Notes
Notes:
svn path=/head/; revision=466367
Diffstat (limited to 'biology/trimadap')
| -rw-r--r-- | biology/trimadap/Makefile | 23 | ||||
| -rw-r--r-- | biology/trimadap/distinfo | 3 | ||||
| -rw-r--r-- | biology/trimadap/files/patch-Makefile | 20 | ||||
| -rw-r--r-- | biology/trimadap/files/patch-kthread.c | 10 | ||||
| -rw-r--r-- | biology/trimadap/pkg-descr | 8 |
5 files changed, 64 insertions, 0 deletions
diff --git a/biology/trimadap/Makefile b/biology/trimadap/Makefile new file mode 100644 index 000000000000..21e8a9b4e149 --- /dev/null +++ b/biology/trimadap/Makefile @@ -0,0 +1,23 @@ +# $FreeBSD$ + +PORTNAME= trimadap +DISTVERSION= 0.1-3 +DISTVERSIONSUFFIX= -gddfef21 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Trim adapter sequences from Illumina data using heuristic rules + +LICENSE= GPLv2 + +USE_GITHUB= yes +GH_ACCOUNT= lh3 + +PLIST_FILES= bin/trimadap-mt + +CFLAGS_i386= -msse2 + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/trimadap-mt ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> diff --git a/biology/trimadap/distinfo b/biology/trimadap/distinfo new file mode 100644 index 000000000000..99e06ce2a75b --- /dev/null +++ b/biology/trimadap/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1522773176 +SHA256 (lh3-trimadap-0.1-3-gddfef21_GH0.tar.gz) = c2c42a3257d37b12be3523ed0d4415bddd401d72b99b05ba4ae33afaa3c3f373 +SIZE (lh3-trimadap-0.1-3-gddfef21_GH0.tar.gz) = 13138 diff --git a/biology/trimadap/files/patch-Makefile b/biology/trimadap/files/patch-Makefile new file mode 100644 index 000000000000..e0d27599fd71 --- /dev/null +++ b/biology/trimadap/files/patch-Makefile @@ -0,0 +1,20 @@ +--- Makefile.orig 2017-02-11 22:31:35 UTC ++++ Makefile +@@ -1,10 +1,12 @@ +-CC=gcc +-CFLAGS=-g -Wall -O2 -Wno-unused-function ++CC ?= gcc ++CFLAGS ?= -g -Wall -O2 -Wno-unused-function ++LDFLAGS += -lz -lm + +-all:trimadap-mt ++all: trimadap-mt + + trimadap-mt:trimadap-mt.c ksw.c kthread.c kseq.h ksw.h +- $(CC) $(CFLAGS) -pthread ksw.c kthread.c trimadap-mt.c -o $@ -lz -lm ++ $(CC) $(CFLAGS) -pthread ksw.c kthread.c trimadap-mt.c -o $@ $(LDFLAGS) + + clean: +- rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* trimadap-mt ++ rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a \ ++ *.dSYM session* trimadap-mt diff --git a/biology/trimadap/files/patch-kthread.c b/biology/trimadap/files/patch-kthread.c new file mode 100644 index 000000000000..5ce6af80ef47 --- /dev/null +++ b/biology/trimadap/files/patch-kthread.c @@ -0,0 +1,10 @@ +--- kthread.c.orig 2017-02-11 22:31:35 UTC ++++ kthread.c +@@ -1,6 +1,7 @@ + #include <pthread.h> + #include <stdlib.h> + #include <limits.h> ++#include <inttypes.h> + + /************ + * kt_for() * diff --git a/biology/trimadap/pkg-descr b/biology/trimadap/pkg-descr new file mode 100644 index 000000000000..f872dd7b2215 --- /dev/null +++ b/biology/trimadap/pkg-descr @@ -0,0 +1,8 @@ +Trimadap is a small tool to trim adapter sequences from Illumina data. It +performs SSE2-SW between each read and each adapter sequence and identifies +adapter sequences with a few heuristic rules which can be found in the +ta_trim1() function in trimadap-mt.c. The default adapters it uses are included +in illumina.txt. These are typical Illumina adapters from paired-end +sequencing. + +WWW: https://github.com/lh3/trimadap |