biology/fastq-trim: Lightening fast sequence read trimmer

Fastq-trim is a lightening fast read trimming tool for QA of
DNA and RNA reads prior to analyses such as RNA-Seq.

5 files changed, 105 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 6712e8a40155..821cf358e8c3 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -45,6 +45,7 @@
     SUBDIR += fastdnaml
     SUBDIR += fastool
     SUBDIR += fastp
+    SUBDIR += fastq-trim
     SUBDIR += fastqc
     SUBDIR += fasttree
     SUBDIR += fastx-toolkit
diff --git a/biology/fastq-trim/Makefile b/biology/fastq-trim/Makefile
new file mode 100644
index 000000000000..7b10097826ba
--- /dev/null
+++ b/biology/fastq-trim/Makefile
@@ -0,0 +1,22 @@
+PORTNAME=	fastq-trim
+DISTVERSION=	0.1.1
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Lightening fast sequence read trimmer
+
+LICENSE=	BSD2CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libbiolibc.so:biology/biolibc libxtend.so:devel/libxtend
+
+USE_GITHUB=	yes
+
+GH_ACCOUNT=	outpaddling
+
+MAKE_ENV=	VERSION=${PORTVERSION}
+
+pre-build:
+	(cd ${WRKSRC} && ${MAKE} LOCALBASE=${LOCALBASE} depend)
+
+.include <bsd.port.mk>
diff --git a/biology/fastq-trim/distinfo b/biology/fastq-trim/distinfo
new file mode 100644
index 000000000000..8b2366479432
--- /dev/null
+++ b/biology/fastq-trim/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1647691961
+SHA256 (outpaddling-fastq-trim-0.1.1_GH0.tar.gz) = ce959484b823f20a5e6e3c493490e71183865d15b6023ee7dc3a5822cc6b176c
+SIZE (outpaddling-fastq-trim-0.1.1_GH0.tar.gz) = 30087
diff --git a/biology/fastq-trim/pkg-descr b/biology/fastq-trim/pkg-descr
new file mode 100644
index 000000000000..e3ec0de0561a
--- /dev/null
+++ b/biology/fastq-trim/pkg-descr
@@ -0,0 +1,4 @@
+Fastq-trim is a hopefully lightening fast read trimming tool for QA of
+DNA and RNA reads prior to analyses such as RNA-Seq.
+
+WWW: https://github.com/outpaddling/Fastq-trim
diff --git a/biology/fastq-trim/pkg-plist b/biology/fastq-trim/pkg-plist
new file mode 100644
index 000000000000..4c55bfdd58f8
--- /dev/null
+++ b/biology/fastq-trim/pkg-plist
@@ -0,0 +1,75 @@
+bin/fastq-trim
+bin/fastq-vis
+include/fastq-trim-accessors.h
+include/fastq-trim-mutators.h
+include/fastq-trim-rvs.h
+include/fastq-trim.h
+lib/libfastq-trim.a
+man/man1/fastq-trim.1.gz
+man/man1/fastq-vis.1.gz
+man/man3/FASTQ_TRIM_ADAPTER1.3.gz
+man/man3/FASTQ_TRIM_ADAPTER1_AE.3.gz
+man/man3/FASTQ_TRIM_ADAPTER2.3.gz
+man/man3/FASTQ_TRIM_ADAPTER2_AE.3.gz
+man/man3/FASTQ_TRIM_ADAPTER_MATCH_FUNCTION.3.gz
+man/man3/FASTQ_TRIM_INFILE1.3.gz
+man/man3/FASTQ_TRIM_INFILE1_AE.3.gz
+man/man3/FASTQ_TRIM_INFILE2.3.gz
+man/man3/FASTQ_TRIM_INFILE2_AE.3.gz
+man/man3/FASTQ_TRIM_INSTREAM1.3.gz
+man/man3/FASTQ_TRIM_INSTREAM1_AE.3.gz
+man/man3/FASTQ_TRIM_INSTREAM2.3.gz
+man/man3/FASTQ_TRIM_INSTREAM2_AE.3.gz
+man/man3/FASTQ_TRIM_MAX_MISMATCH_PERCENT.3.gz
+man/man3/FASTQ_TRIM_MIN_LENGTH.3.gz
+man/man3/FASTQ_TRIM_MIN_MATCH.3.gz
+man/man3/FASTQ_TRIM_MIN_QUAL.3.gz
+man/man3/FASTQ_TRIM_OUTFILE1.3.gz
+man/man3/FASTQ_TRIM_OUTFILE1_AE.3.gz
+man/man3/FASTQ_TRIM_OUTFILE2.3.gz
+man/man3/FASTQ_TRIM_OUTFILE2_AE.3.gz
+man/man3/FASTQ_TRIM_OUTSTREAM1.3.gz
+man/man3/FASTQ_TRIM_OUTSTREAM1_AE.3.gz
+man/man3/FASTQ_TRIM_OUTSTREAM2.3.gz
+man/man3/FASTQ_TRIM_OUTSTREAM2_AE.3.gz
+man/man3/FASTQ_TRIM_PHRED_BASE.3.gz
+man/man3/FASTQ_TRIM_POLYA_MIN_LEN.3.gz
+man/man3/FASTQ_TRIM_VERBOSE.3.gz
+man/man3/fastq_trim_set_adapter1.3.gz
+man/man3/fastq_trim_set_adapter1_ae.3.gz
+man/man3/fastq_trim_set_adapter1_cpy.3.gz
+man/man3/fastq_trim_set_adapter2.3.gz
+man/man3/fastq_trim_set_adapter2_ae.3.gz
+man/man3/fastq_trim_set_adapter2_cpy.3.gz
+man/man3/fastq_trim_set_adapter_match_function.3.gz
+man/man3/fastq_trim_set_infile1.3.gz
+man/man3/fastq_trim_set_infile1_ae.3.gz
+man/man3/fastq_trim_set_infile1_cpy.3.gz
+man/man3/fastq_trim_set_infile2.3.gz
+man/man3/fastq_trim_set_infile2_ae.3.gz
+man/man3/fastq_trim_set_infile2_cpy.3.gz
+man/man3/fastq_trim_set_instream1.3.gz
+man/man3/fastq_trim_set_instream1_ae.3.gz
+man/man3/fastq_trim_set_instream1_cpy.3.gz
+man/man3/fastq_trim_set_instream2.3.gz
+man/man3/fastq_trim_set_instream2_ae.3.gz
+man/man3/fastq_trim_set_instream2_cpy.3.gz
+man/man3/fastq_trim_set_max_mismatch_percent.3.gz
+man/man3/fastq_trim_set_min_length.3.gz
+man/man3/fastq_trim_set_min_match.3.gz
+man/man3/fastq_trim_set_min_qual.3.gz
+man/man3/fastq_trim_set_outfile1.3.gz
+man/man3/fastq_trim_set_outfile1_ae.3.gz
+man/man3/fastq_trim_set_outfile1_cpy.3.gz
+man/man3/fastq_trim_set_outfile2.3.gz
+man/man3/fastq_trim_set_outfile2_ae.3.gz
+man/man3/fastq_trim_set_outfile2_cpy.3.gz
+man/man3/fastq_trim_set_outstream1.3.gz
+man/man3/fastq_trim_set_outstream1_ae.3.gz
+man/man3/fastq_trim_set_outstream1_cpy.3.gz
+man/man3/fastq_trim_set_outstream2.3.gz
+man/man3/fastq_trim_set_outstream2_ae.3.gz
+man/man3/fastq_trim_set_outstream2_cpy.3.gz
+man/man3/fastq_trim_set_phred_base.3.gz
+man/man3/fastq_trim_set_polya_min_len.3.gz
+man/man3/fastq_trim_set_verbose.3.gz