From 27648ff947aab8d3bdb2710df17cd329d2e450f9 Mon Sep 17 00:00:00 2001 From: Jason Bacon Date: Mon, 7 Jan 2019 19:56:46 -0600 Subject: [PATCH] fastx-toolkit: CLI tools for Short-Reads FASTA/FASTQ files preprocessing --- Makefile | 1 + fastx-toolkit/DESCR | 2 ++ fastx-toolkit/Makefile | 31 +++++++++++++++++++ fastx-toolkit/PLIST | 24 ++++++++++++++ fastx-toolkit/distinfo | 7 +++++ .../patches/patch-src_libfastx_fastx.h | 23 ++++++++++++++ 6 files changed, 88 insertions(+) create mode 100644 fastx-toolkit/DESCR create mode 100644 fastx-toolkit/Makefile create mode 100644 fastx-toolkit/PLIST create mode 100644 fastx-toolkit/distinfo create mode 100644 fastx-toolkit/patches/patch-src_libfastx_fastx.h diff --git a/Makefile b/Makefile index 9d4d329d8f..9108c058ce 100644 --- a/Makefile +++ b/Makefile @@ -758,6 +758,7 @@ SUBDIR+= fastool SUBDIR+= fastqc SUBDIR+= fastrpc SUBDIR+= fasttree +SUBDIR+= fastx-toolkit SUBDIR+= fbida SUBDIR+= fbpager SUBDIR+= fbpanel diff --git a/fastx-toolkit/DESCR b/fastx-toolkit/DESCR new file mode 100644 index 0000000000..55b9642bb4 --- /dev/null +++ b/fastx-toolkit/DESCR @@ -0,0 +1,2 @@ +The FASTX-Toolkit is a collection of command line tools for Short-Reads +FASTA/FASTQ files preprocessing. diff --git a/fastx-toolkit/Makefile b/fastx-toolkit/Makefile new file mode 100644 index 0000000000..a8b608116c --- /dev/null +++ b/fastx-toolkit/Makefile @@ -0,0 +1,31 @@ +# $NetBSD$ +# +########################################################### +# Generated by fbsd2pkg # +# Mon Jan 7 19:28:31 CST 2019 # +########################################################### + +DISTNAME= fastx_toolkit-0.0.14 +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_GITHUB:=agordon/} +GITHUB_PROJECT= fastx_toolkit + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= http://hannonlab.cshl.edu/fastx_toolkit/ +COMMENT= CLI tools for Short-Reads FASTA/FASTQ files preprocessing +LICENSE= gnu-agpl-v3 + +USE_LANGUAGES= c c++ +USE_TOOLS+= autoconf automake autoreconf bash pkg-config perl:run +USE_LIBTOOL= yes +GNU_CONFIGURE= yes +REPLACE_PERL+= scripts/*.pl +REPLACE_BASH+= scripts/fastq_quality_boxplot_graph.sh +REPLACE_BASH+= scripts/fastx_nucleotide_distribution_graph.sh +REPLACE_BASH+= scripts/fastx_nucleotide_distribution_line_graph.sh + +pre-configure: + cd ${WRKSRC} && autoreconf -if + +.include "../../wip/gtextutils/buildlink3.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/fastx-toolkit/PLIST b/fastx-toolkit/PLIST new file mode 100644 index 0000000000..ed21b2092d --- /dev/null +++ b/fastx-toolkit/PLIST @@ -0,0 +1,24 @@ +@comment $NetBSD$ +bin/fasta_clipping_histogram.pl +bin/fasta_formatter +bin/fasta_nucleotide_changer +bin/fastq_masker +bin/fastq_quality_boxplot_graph.sh +bin/fastq_quality_converter +bin/fastq_quality_filter +bin/fastq_quality_trimmer +bin/fastq_to_fasta +bin/fastx_artifacts_filter +bin/fastx_barcode_splitter.pl +bin/fastx_clipper +bin/fastx_collapser +bin/fastx_nucleotide_distribution_graph.sh +bin/fastx_nucleotide_distribution_line_graph.sh +bin/fastx_quality_stats +bin/fastx_renamer +bin/fastx_reverse_complement +bin/fastx_trimmer +bin/fastx_uncollapser +share/aclocal/ax_c_long_long.m4 +share/aclocal/ax_cxx_compile_stdcxx_11.m4 +share/aclocal/ax_cxx_header_stdcxx_tr1.m4 diff --git a/fastx-toolkit/distinfo b/fastx-toolkit/distinfo new file mode 100644 index 0000000000..e1709ea494 --- /dev/null +++ b/fastx-toolkit/distinfo @@ -0,0 +1,7 @@ +$NetBSD$ + +SHA1 (fastx_toolkit-0.0.14.tar.gz) = ce008d34469afd48f4012d37797f91972a8f72cf +RMD160 (fastx_toolkit-0.0.14.tar.gz) = 759a34c6e30f96eeef415dc832ec4a518866be09 +SHA512 (fastx_toolkit-0.0.14.tar.gz) = d8e18a3622dcdb5b543fcb787818ac468b26341d5d4409326c951b504862eb44226f625228985bec6fb2e02c45f9a127591a312dadd53415337a7c09f6229708 +Size (fastx_toolkit-0.0.14.tar.gz) = 259576 bytes +SHA1 (patch-src_libfastx_fastx.h) = 5a387ac575a5269bc03e3f09ab752889efb8870c diff --git a/fastx-toolkit/patches/patch-src_libfastx_fastx.h b/fastx-toolkit/patches/patch-src_libfastx_fastx.h new file mode 100644 index 0000000000..12a988432e --- /dev/null +++ b/fastx-toolkit/patches/patch-src_libfastx_fastx.h @@ -0,0 +1,23 @@ +$NetBSD$ + +# Limit packing to this one structure to avoid compatibility issues + +--- src/libfastx/fastx.h.orig 2018-05-16 14:50:08 UTC ++++ src/libfastx/fastx.h +@@ -58,7 +58,7 @@ typedef enum { + OUTPUT_SAME_AS_INPUT=3 + } OUTPUT_FILE_TYPE; + +-#pragma pack(1) ++#pragma pack(push,1) + typedef struct + { + /* Record data - common for FASTA/FASTQ */ +@@ -115,6 +115,7 @@ typedef struct + FILE* input; + FILE* output; + } FASTX ; ++#pragma pack(pop) + + + void fastx_init_reader(FASTX *pFASTX, const char* filename,