CVS commit: pkgsrc/biology/fastq-trim

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sun Nov  6 22:49:37 UTC 2022

Added Files:
        pkgsrc/biology/fastq-trim: DESCR Makefile PLIST distinfo

Log Message:
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.  it runs in a fraction of the time required
by popular trimmers and uses only a few megabytes of RAM, so it will run
almost entirely in cache.  The design supports adding any number of alignment
functions, so it can be easily adapted to any trimming needs.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/fastq-trim/DESCR \
    pkgsrc/biology/fastq-trim/Makefile pkgsrc/biology/fastq-trim/PLIST \
    pkgsrc/biology/fastq-trim/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/fastq-trim/DESCR
diff -u /dev/null pkgsrc/biology/fastq-trim/DESCR:1.1
--- /dev/null   Sun Nov  6 22:49:37 2022
+++ pkgsrc/biology/fastq-trim/DESCR     Sun Nov  6 22:49:37 2022
@@ -0,0 +1,5 @@
+Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads
+prior to analyses such as RNA-Seq.  it runs in a fraction of the time required
+by popular trimmers and uses only a few megabytes of RAM, so it will run
+almost entirely in cache.  The design supports adding any number of alignment
+functions, so it can be easily adapted to any trimming needs.
Index: pkgsrc/biology/fastq-trim/Makefile
diff -u /dev/null pkgsrc/biology/fastq-trim/Makefile:1.1
--- /dev/null   Sun Nov  6 22:49:37 2022
+++ pkgsrc/biology/fastq-trim/Makefile  Sun Nov  6 22:49:37 2022
@@ -0,0 +1,21 @@
+# $NetBSD: Makefile,v 1.1 2022/11/06 22:49:37 bacon Exp $
+
+DISTNAME=      fastq-trim-0.1.1.16
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=outpaddling/}
+GITHUB_TAG=    58a016f250a9b785bfed574ce471ec7e23cdaa4a
+
+MAINTAINER=    bacon%NetBSD.org@localhost
+HOMEPAGE=      https://github.com/outpaddling/Fastq-trim
+COMMENT=       Lightening fast sequence read trimmer
+LICENSE=       2-clause-bsd
+
+MAKE_ENV=      VERSION=${PKGVERSION}
+
+LDFLAGS.SunOS= -lresolv
+
+pre-build:
+       (cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend)
+
+.include "../../biology/biolibc/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/fastq-trim/PLIST
diff -u /dev/null pkgsrc/biology/fastq-trim/PLIST:1.1
--- /dev/null   Sun Nov  6 22:49:37 2022
+++ pkgsrc/biology/fastq-trim/PLIST     Sun Nov  6 22:49:37 2022
@@ -0,0 +1,76 @@
+@comment $NetBSD: PLIST,v 1.1 2022/11/06 22:49:37 bacon Exp $
+bin/fastq-scum
+bin/fastq-trim
+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-scum.1
+man/man1/fastq-trim.1
+man/man3/FASTQ_TRIM_ADAPTER1.3
+man/man3/FASTQ_TRIM_ADAPTER1_AE.3
+man/man3/FASTQ_TRIM_ADAPTER2.3
+man/man3/FASTQ_TRIM_ADAPTER2_AE.3
+man/man3/FASTQ_TRIM_ADAPTER_MATCH_FUNCTION.3
+man/man3/FASTQ_TRIM_INFILE1.3
+man/man3/FASTQ_TRIM_INFILE1_AE.3
+man/man3/FASTQ_TRIM_INFILE2.3
+man/man3/FASTQ_TRIM_INFILE2_AE.3
+man/man3/FASTQ_TRIM_INSTREAM1.3
+man/man3/FASTQ_TRIM_INSTREAM1_AE.3
+man/man3/FASTQ_TRIM_INSTREAM2.3
+man/man3/FASTQ_TRIM_INSTREAM2_AE.3
+man/man3/FASTQ_TRIM_MAX_MISMATCH_PERCENT.3
+man/man3/FASTQ_TRIM_MIN_LENGTH.3
+man/man3/FASTQ_TRIM_MIN_MATCH.3
+man/man3/FASTQ_TRIM_MIN_QUAL.3
+man/man3/FASTQ_TRIM_OUTFILE1.3
+man/man3/FASTQ_TRIM_OUTFILE1_AE.3
+man/man3/FASTQ_TRIM_OUTFILE2.3
+man/man3/FASTQ_TRIM_OUTFILE2_AE.3
+man/man3/FASTQ_TRIM_OUTSTREAM1.3
+man/man3/FASTQ_TRIM_OUTSTREAM1_AE.3
+man/man3/FASTQ_TRIM_OUTSTREAM2.3
+man/man3/FASTQ_TRIM_OUTSTREAM2_AE.3
+man/man3/FASTQ_TRIM_PHRED_BASE.3
+man/man3/FASTQ_TRIM_POLYA_MIN_LEN.3
+man/man3/FASTQ_TRIM_VERBOSE.3
+man/man3/fastq_trim_set_adapter1.3
+man/man3/fastq_trim_set_adapter1_ae.3
+man/man3/fastq_trim_set_adapter1_cpy.3
+man/man3/fastq_trim_set_adapter2.3
+man/man3/fastq_trim_set_adapter2_ae.3
+man/man3/fastq_trim_set_adapter2_cpy.3
+man/man3/fastq_trim_set_adapter_match_function.3
+man/man3/fastq_trim_set_infile1.3
+man/man3/fastq_trim_set_infile1_ae.3
+man/man3/fastq_trim_set_infile1_cpy.3
+man/man3/fastq_trim_set_infile2.3
+man/man3/fastq_trim_set_infile2_ae.3
+man/man3/fastq_trim_set_infile2_cpy.3
+man/man3/fastq_trim_set_instream1.3
+man/man3/fastq_trim_set_instream1_ae.3
+man/man3/fastq_trim_set_instream1_cpy.3
+man/man3/fastq_trim_set_instream2.3
+man/man3/fastq_trim_set_instream2_ae.3
+man/man3/fastq_trim_set_instream2_cpy.3
+man/man3/fastq_trim_set_max_mismatch_percent.3
+man/man3/fastq_trim_set_min_length.3
+man/man3/fastq_trim_set_min_match.3
+man/man3/fastq_trim_set_min_qual.3
+man/man3/fastq_trim_set_outfile1.3
+man/man3/fastq_trim_set_outfile1_ae.3
+man/man3/fastq_trim_set_outfile1_cpy.3
+man/man3/fastq_trim_set_outfile2.3
+man/man3/fastq_trim_set_outfile2_ae.3
+man/man3/fastq_trim_set_outfile2_cpy.3
+man/man3/fastq_trim_set_outstream1.3
+man/man3/fastq_trim_set_outstream1_ae.3
+man/man3/fastq_trim_set_outstream1_cpy.3
+man/man3/fastq_trim_set_outstream2.3
+man/man3/fastq_trim_set_outstream2_ae.3
+man/man3/fastq_trim_set_outstream2_cpy.3
+man/man3/fastq_trim_set_phred_base.3
+man/man3/fastq_trim_set_polya_min_len.3
+man/man3/fastq_trim_set_verbose.3
Index: pkgsrc/biology/fastq-trim/distinfo
diff -u /dev/null pkgsrc/biology/fastq-trim/distinfo:1.1
--- /dev/null   Sun Nov  6 22:49:37 2022
+++ pkgsrc/biology/fastq-trim/distinfo  Sun Nov  6 22:49:37 2022
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1 2022/11/06 22:49:37 bacon Exp $
+
+BLAKE2s (fastq-trim-0.1.1.16-58a016f250a9b785bfed574ce471ec7e23cdaa4a.tar.gz) = a2383eed63d5bb75dbb8c1ca2f6a5f08f737cb6243772e87d0477938cc3440f7
+SHA512 (fastq-trim-0.1.1.16-58a016f250a9b785bfed574ce471ec7e23cdaa4a.tar.gz) = 
26d0bf350bac6b3bbfb98d35e6587a1b58a9f353f376f676d97a9c6ff36e41ea05a906eeee2089834f05e26121b7014fd93ef5ba732eb8f8d977edfacaa01225
+Size (fastq-trim-0.1.1.16-58a016f250a9b785bfed574ce471ec7e23cdaa4a.tar.gz) = 29819 bytes