The FASTX-Toolkit is a collection of command line tools for Short-Reads

FASTA/FASTQ files preprocessing.

WWW: http://hannonlab.cshl.edu/fastx_toolkit/

PR:		203318
Submitted by:	Jason Bacon <jwbacon@tds.net>

5 files changed, 57 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 3d9eb0b..77e6807 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -20,6 +20,7 @@
     SUBDIR += fasta
     SUBDIR += fasta3
     SUBDIR += fastdnaml
+    SUBDIR += fastx-toolkit
     SUBDIR += fluctuate
     SUBDIR += garlic
     SUBDIR += gff2ps
diff --git a/biology/fastx-toolkit/Makefile b/biology/fastx-toolkit/Makefile
new file mode 100644
index 0000000..b93aa50
--- /dev/null
+++ b/biology/fastx-toolkit/Makefile
@@ -0,0 +1,27 @@
+# Created by: Jason Bacon <jwbacon@tds.net>
+# $FreeBSD$
+
+PORTNAME=	fastx_toolkit
+PORTVERSION=	0.0.14
+CATEGORIES=	biology
+
+MAINTAINER=	jwbacon@tds.net
+COMMENT=	CLI tools for Short-Reads FASTA/FASTQ files preprocessing
+
+LICENSE=	AGPLv3
+
+LIB_DEPENDS=	libgtextutils.so:${PORTSDIR}/biology/libgtextutils
+
+USES=		autoreconf libtool perl5 pkgconfig shebangfix tar:bzip2
+USE_PERL5=	run
+SHEBANG_FILES=	scripts/*.pl
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	agordon
+GH_PROJECT=	${PORTNAME}
+
+GNU_CONFIGURE=	yes
+
+CONFIGURE_ENV+=	PKG_CONFIG_PATH=${PREFIX}/lib/pkgconfig
+
+.include <bsd.port.mk>
diff --git a/biology/fastx-toolkit/distinfo b/biology/fastx-toolkit/distinfo
new file mode 100644
index 0000000..9adae3e
--- /dev/null
+++ b/biology/fastx-toolkit/distinfo
@@ -0,0 +1,2 @@
+SHA256 (agordon-fastx_toolkit-0.0.14_GH0.tar.bz2) = af4f9fe59f8c91bdd2d735bdac1fd89f0549b2bc759313fe3b86948056aad1aa
+SIZE (agordon-fastx_toolkit-0.0.14_GH0.tar.bz2) = 259576
diff --git a/biology/fastx-toolkit/pkg-descr b/biology/fastx-toolkit/pkg-descr
new file mode 100644
index 0000000..b5adb7e
--- /dev/null
+++ b/biology/fastx-toolkit/pkg-descr
@@ -0,0 +1,4 @@
+The FASTX-Toolkit is a collection of command line tools for Short-Reads
+FASTA/FASTQ files preprocessing.
+
+WWW: http://hannonlab.cshl.edu/fastx_toolkit/
diff --git a/biology/fastx-toolkit/pkg-plist b/biology/fastx-toolkit/pkg-plist
new file mode 100644
index 0000000..828bb7c
--- /dev/null
+++ b/biology/fastx-toolkit/pkg-plist
@@ -0,0 +1,23 @@
+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