biology/stacks: import stacks-2.2

Stacks is a software pipeline for building loci from short-read sequences, such
as those generated on the Illumina platform. Stacks was developed to work with
restriction enzyme-based data, such as RAD-seq, for the purpose of building
genetic maps and conducting population genomics and phylogeography.

4 files changed, 102 insertions, 0 deletions

diff --git a/biology/stacks/DESCR b/biology/stacks/DESCR
new file mode 100644
index 00000000000..91c14fbc8df
--- /dev/null
+++ b/biology/stacks/DESCR
@@ -0,0 +1,4 @@
+Stacks is a software pipeline for building loci from short-read sequences, such
+as those generated on the Illumina platform. Stacks was developed to work with
+restriction enzyme-based data, such as RAD-seq, for the purpose of building
+genetic maps and conducting population genomics and phylogeography.
diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile
new file mode 100644
index 00000000000..ed32c60154f
--- /dev/null
+++ b/biology/stacks/Makefile
@@ -0,0 +1,26 @@
+# $NetBSD: Makefile,v 1.1 2018/12/22 21:52:06 bacon Exp $
+
+DISTNAME=	stacks-2.2
+CATEGORIES=	biology
+MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
+
+MAINTAINER=	bacon@NetBSD.org
+HOMEPAGE=	http://catchenlab.life.illinois.edu/stacks/
+COMMENT=	Software pipeline for building loci from short-read sequences
+LICENSE=	gnu-gpl-v2
+
+USE_LANGUAGES=	c c++14
+GCC_REQD+=	4.9
+USE_TOOLS+=	bash perl:run
+GNU_CONFIGURE=	yes
+
+REPLACE_BASH=	scripts/stacks-integrate-alignments scripts/stacks-gdb
+REPLACE_BASH+=	scripts/stacks-dist-extract
+REPLACE_PERL=	scripts/*.pl
+REPLACE_PYTHON=	scripts/*.py
+
+CFLAGS+=	-fopenmp
+
+.include "../../lang/python/application.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/stacks/PLIST b/biology/stacks/PLIST
new file mode 100644
index 00000000000..357dc2052af
--- /dev/null
+++ b/biology/stacks/PLIST
@@ -0,0 +1,66 @@
+@comment $NetBSD: PLIST,v 1.1 2018/12/22 21:52:06 bacon Exp $
+bin/clone_filter
+bin/count_fixed_catalog_snps.py
+bin/cstacks
+bin/denovo_map.pl
+bin/gstacks
+bin/integrate_alignments.py
+bin/kmer_filter
+bin/phasedstacks
+bin/populations
+bin/process_radtags
+bin/process_shortreads
+bin/ref_map.pl
+bin/sstacks
+bin/stacks-dist-extract
+bin/stacks-gdb
+bin/stacks-integrate-alignments
+bin/tsv2bam
+bin/ustacks
+share/stacks/php/CatalogClass.php
+share/stacks/php/Locus.php
+share/stacks/php/ajax.js
+share/stacks/php/annotate.js
+share/stacks/php/annotate_marker.php
+share/stacks/php/catalog.php
+share/stacks/php/catalog_genotypes.php
+share/stacks/php/constants.php.dist
+share/stacks/php/correct_genotype.php
+share/stacks/php/correct_genotypes.php
+share/stacks/php/db_functions.php
+share/stacks/php/export.js
+share/stacks/php/export_batch.php
+share/stacks/php/fst_view.php
+share/stacks/php/hapstat_view.php
+share/stacks/php/header.php
+share/stacks/php/images/caret-d.png
+share/stacks/php/images/caret-u.png
+share/stacks/php/images/excel_icon.png
+share/stacks/php/images/l-arrow-disabled.png
+share/stacks/php/images/l-arrow.png
+share/stacks/php/images/r-arrow-disabled.png
+share/stacks/php/images/r-arrow.png
+share/stacks/php/images/stacks_bg.png
+share/stacks/php/images/stacks_logo_rev_small.png
+share/stacks/php/index.php
+share/stacks/php/last_modified.php
+share/stacks/php/phist_view.php
+share/stacks/php/pop_view.php
+share/stacks/php/population_view.js
+share/stacks/php/samples.php
+share/stacks/php/sequence_blast.php
+share/stacks/php/stack_view.php
+share/stacks/php/stacks.css
+share/stacks/php/stacks.js
+share/stacks/php/stacks_functions.php
+share/stacks/php/sumstat_view.php
+share/stacks/php/tag.php
+share/stacks/php/tags.php
+share/stacks/php/version.php
+share/stacks/php/view_sequence.php
+share/stacks/sql/catalog_index.sql
+share/stacks/sql/chr_index.sql
+share/stacks/sql/mysql.cnf.dist
+share/stacks/sql/stacks.sql
+share/stacks/sql/tag_index.sql
+@pkgdir share/stacks/php/export
diff --git a/biology/stacks/distinfo b/biology/stacks/distinfo
new file mode 100644
index 00000000000..65fce4d9111
--- /dev/null
+++ b/biology/stacks/distinfo
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2018/12/22 21:52:06 bacon Exp $
+
+SHA1 (stacks-2.2.tar.gz) = ee99798378b906f356c23da0073d0361440263bf
+RMD160 (stacks-2.2.tar.gz) = 2f5097c668d9662dbbec705fe3bf00216c11d388
+SHA512 (stacks-2.2.tar.gz) = f1cffd12313fed1c171af46f9fb501373b43d57cd3004edae1034074f43169d43398743cf625ffa21be412c808ba1168513a33c63377ee13dd056406fa222095
+Size (stacks-2.2.tar.gz) = 10822973 bytes