From 8fc22a90cf71336a29bf194b3f828677d4aa3e60 Mon Sep 17 00:00:00 2001 From: bacon Date: Tue, 5 Apr 2022 18:48:57 +0000 Subject: biology/fastx-toolkit: CLI tools for FASTA/FASTQ files preprocessing The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. --- biology/fastx-toolkit/DESCR | 2 ++ biology/fastx-toolkit/Makefile | 27 ++++++++++++++++++++++ biology/fastx-toolkit/PLIST | 21 +++++++++++++++++ biology/fastx-toolkit/distinfo | 8 +++++++ biology/fastx-toolkit/patches/patch-m4_Makefile.am | 14 +++++++++++ ...patch-src_fasta__formatter_fasta__formatter.cpp | 14 +++++++++++ .../patches/patch-src_libfastx_fastx.h | 23 ++++++++++++++++++ 7 files changed, 109 insertions(+) create mode 100644 biology/fastx-toolkit/DESCR create mode 100644 biology/fastx-toolkit/Makefile create mode 100644 biology/fastx-toolkit/PLIST create mode 100644 biology/fastx-toolkit/distinfo create mode 100644 biology/fastx-toolkit/patches/patch-m4_Makefile.am create mode 100644 biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp create mode 100644 biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h (limited to 'biology') diff --git a/biology/fastx-toolkit/DESCR b/biology/fastx-toolkit/DESCR new file mode 100644 index 00000000000..e3e97cad062 --- /dev/null +++ b/biology/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/biology/fastx-toolkit/Makefile b/biology/fastx-toolkit/Makefile new file mode 100644 index 00000000000..cba4d57e44a --- /dev/null +++ b/biology/fastx-toolkit/Makefile @@ -0,0 +1,27 @@ +# $NetBSD: Makefile,v 1.1 2022/04/05 18:48:57 bacon Exp $ + +DISTNAME= fastx-toolkit-0.0.14.6 +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_GITHUB:=agordon/} +GITHUB_PROJECT= fastx_toolkit +GITHUB_TAG= ea0ca83ba24dce80c20ca589b838a281fe5deb0c + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= https://github.com/agordon/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: + ${RUN} cd ${WRKSRC} && autoreconf -vif + +.include "../../devel/libgtextutils/buildlink3.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/fastx-toolkit/PLIST b/biology/fastx-toolkit/PLIST new file mode 100644 index 00000000000..04e3aedde22 --- /dev/null +++ b/biology/fastx-toolkit/PLIST @@ -0,0 +1,21 @@ +@comment $NetBSD: PLIST,v 1.1 2022/04/05 18:48:57 bacon Exp $ +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 diff --git a/biology/fastx-toolkit/distinfo b/biology/fastx-toolkit/distinfo new file mode 100644 index 00000000000..ae2ae8a4960 --- /dev/null +++ b/biology/fastx-toolkit/distinfo @@ -0,0 +1,8 @@ +$NetBSD: distinfo,v 1.1 2022/04/05 18:48:57 bacon Exp $ + +BLAKE2s (fastx-toolkit-0.0.14.6-ea0ca83ba24dce80c20ca589b838a281fe5deb0c.tar.gz) = 973b56d722a2796aa28a04de56ef9273ce5a99fae5cf40bdbf9ef796acb2b6ef +SHA512 (fastx-toolkit-0.0.14.6-ea0ca83ba24dce80c20ca589b838a281fe5deb0c.tar.gz) = bb9cc9685a37e0a88b5110ad48856d4160dc1a29e6b76f8cdf78baf12a9cea97c35f711b1aef270bba5d44b42c8e6bcc31ef9eae239de785fe1bd38cd4994d3e +Size (fastx-toolkit-0.0.14.6-ea0ca83ba24dce80c20ca589b838a281fe5deb0c.tar.gz) = 259875 bytes +SHA1 (patch-m4_Makefile.am) = f8cb138860f0a3708a6690ea6cd33302b35bce76 +SHA1 (patch-src_fasta__formatter_fasta__formatter.cpp) = 5fc622320186c5415cbcc4ae97cfc24f68983949 +SHA1 (patch-src_libfastx_fastx.h) = 5a387ac575a5269bc03e3f09ab752889efb8870c diff --git a/biology/fastx-toolkit/patches/patch-m4_Makefile.am b/biology/fastx-toolkit/patches/patch-m4_Makefile.am new file mode 100644 index 00000000000..e85265c188a --- /dev/null +++ b/biology/fastx-toolkit/patches/patch-m4_Makefile.am @@ -0,0 +1,14 @@ +$NetBSD: patch-m4_Makefile.am,v 1.1 2022/04/05 18:48:57 bacon Exp $ + +Do not install unrelated m4 files. + +--- m4/Makefile.am.orig 2017-08-14 18:08:32.000000000 +0000 ++++ m4/Makefile.am +@@ -17,6 +17,6 @@ m4macros = ax_c_long_long.m4 \ + ax_cxx_header_stdcxx_tr1.m4 + + # The following is boilerplate +-m4data_DATA = $(m4macros) ++#m4data_DATA = $(m4macros) + EXTRA_DIST = $(m4data_DATA) + diff --git a/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp b/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp new file mode 100644 index 00000000000..e2a5756115f --- /dev/null +++ b/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp @@ -0,0 +1,14 @@ +$NetBSD: patch-src_fasta__formatter_fasta__formatter.cpp,v 1.1 2022/04/05 18:48:57 bacon Exp $ + +# Silence compile error + +--- src/fasta_formatter/fasta_formatter.cpp.orig 2022-04-03 12:45:51.295476843 +0000 ++++ src/fasta_formatter/fasta_formatter.cpp +@@ -103,6 +103,7 @@ void parse_command_line(int argc, char* + switch(opt) { + case 'h': + usage(); ++ break; + + case 'i': + input_filename = optarg; diff --git a/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h b/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h new file mode 100644 index 00000000000..0a25126f420 --- /dev/null +++ b/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h @@ -0,0 +1,23 @@ +$NetBSD: patch-src_libfastx_fastx.h,v 1.1 2022/04/05 18:48:57 bacon Exp $ + +# 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, -- cgit v1.2.3