fastx-toolkit: CLI tools for Short-Reads FASTA/FASTQ files preprocessing

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Jan 7 19:56:46 2019 -0600
Changeset:	27648ff947aab8d3bdb2710df17cd329d2e450f9

Modified Files:
	Makefile
Added Files:
	fastx-toolkit/DESCR
	fastx-toolkit/Makefile
	fastx-toolkit/PLIST
	fastx-toolkit/distinfo
	fastx-toolkit/patches/patch-src_libfastx_fastx.h

Log Message:
fastx-toolkit: CLI tools for Short-Reads FASTA/FASTQ files preprocessing

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=27648ff947aab8d3bdb2710df17cd329d2e450f9

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

diffstat:
 Makefile                                         |  1 +
 fastx-toolkit/DESCR                              |  2 ++
 fastx-toolkit/Makefile                           | 31 ++++++++++++++++++++++++
 fastx-toolkit/PLIST                              | 24 ++++++++++++++++++
 fastx-toolkit/distinfo                           |  7 ++++++
 fastx-toolkit/patches/patch-src_libfastx_fastx.h | 23 ++++++++++++++++++
 6 files changed, 88 insertions(+)

diffs:
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@localhost
+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,