Date: Sat, 19 Mar 2022 12:26:39 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: a47115b9cad4 - main - biology/fastq-trim: Lightening fast sequence read trimmer Message-ID: <202203191226.22JCQdNo059833@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=a47115b9cad4784d5923f6a6e3d0fbef28623e8f commit a47115b9cad4784d5923f6a6e3d0fbef28623e8f Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2022-03-19 12:25:58 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2022-03-19 12:25:58 +0000 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. --- biology/Makefile | 1 + biology/fastq-trim/Makefile | 22 +++++++++++++ biology/fastq-trim/distinfo | 3 ++ biology/fastq-trim/pkg-descr | 4 +++ biology/fastq-trim/pkg-plist | 75 ++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 105 insertions(+) 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
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