CVS commit: pkgsrc/biology/fastx-toolkit

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Tue Apr  5 18:48:57 UTC 2022

Added Files:
        pkgsrc/biology/fastx-toolkit: DESCR Makefile PLIST distinfo
        pkgsrc/biology/fastx-toolkit/patches: patch-m4_Makefile.am
            patch-src_fasta__formatter_fasta__formatter.cpp
            patch-src_libfastx_fastx.h

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/fastx-toolkit/DESCR \
    pkgsrc/biology/fastx-toolkit/Makefile pkgsrc/biology/fastx-toolkit/PLIST \
    pkgsrc/biology/fastx-toolkit/distinfo
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/biology/fastx-toolkit/patches/patch-m4_Makefile.am \
    pkgsrc/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp \
    pkgsrc/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h

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

Added files:

Index: pkgsrc/biology/fastx-toolkit/DESCR
diff -u /dev/null pkgsrc/biology/fastx-toolkit/DESCR:1.1
--- /dev/null   Tue Apr  5 18:48:57 2022
+++ pkgsrc/biology/fastx-toolkit/DESCR  Tue Apr  5 18:48:57 2022
@@ -0,0 +1,2 @@
+The FASTX-Toolkit is a collection of command line tools for
+Short-Reads FASTA/FASTQ files preprocessing.
Index: pkgsrc/biology/fastx-toolkit/Makefile
diff -u /dev/null pkgsrc/biology/fastx-toolkit/Makefile:1.1
--- /dev/null   Tue Apr  5 18:48:57 2022
+++ pkgsrc/biology/fastx-toolkit/Makefile       Tue Apr  5 18:48:57 2022
@@ -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@localhost
+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"
Index: pkgsrc/biology/fastx-toolkit/PLIST
diff -u /dev/null pkgsrc/biology/fastx-toolkit/PLIST:1.1
--- /dev/null   Tue Apr  5 18:48:57 2022
+++ pkgsrc/biology/fastx-toolkit/PLIST  Tue Apr  5 18:48:57 2022
@@ -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
Index: pkgsrc/biology/fastx-toolkit/distinfo
diff -u /dev/null pkgsrc/biology/fastx-toolkit/distinfo:1.1
--- /dev/null   Tue Apr  5 18:48:57 2022
+++ pkgsrc/biology/fastx-toolkit/distinfo       Tue Apr  5 18:48:57 2022
@@ -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

Index: pkgsrc/biology/fastx-toolkit/patches/patch-m4_Makefile.am
diff -u /dev/null pkgsrc/biology/fastx-toolkit/patches/patch-m4_Makefile.am:1.1
--- /dev/null   Tue Apr  5 18:48:57 2022
+++ pkgsrc/biology/fastx-toolkit/patches/patch-m4_Makefile.am   Tue Apr  5 18:48:57 2022
@@ -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 = $(m4data_DATA) 
+ 
Index: pkgsrc/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp
diff -u /dev/null pkgsrc/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp:1.1
--- /dev/null   Tue Apr  5 18:48:57 2022
+++ pkgsrc/biology/fastx-toolkit/patches/patch-src_fasta__formatter_fasta__formatter.cpp        Tue Apr  5 18:48:57 2022
@@ -0,0 +1,14 @@
+$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;
Index: pkgsrc/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h
diff -u /dev/null pkgsrc/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h:1.1
--- /dev/null   Tue Apr  5 18:48:57 2022
+++ pkgsrc/biology/fastx-toolkit/patches/patch-src_libfastx_fastx.h     Tue Apr  5 18:48:57 2022
@@ -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,