stacks2: Software pipeline for building loci from short-read sequences

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Dec 6 20:57:02 2018 -0600
Changeset:	e31f4c7677911eff208d87ef7d676a2edd14a179

Modified Files:
	Makefile
Added Files:
	stacks2/DESCR
	stacks2/Makefile
	stacks2/PLIST
	stacks2/distinfo

Log Message:
stacks2: Software pipeline for building loci from short-read sequences

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e31f4c7677911eff208d87ef7d676a2edd14a179

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

diffstat:
 Makefile         |  2 ++
 stacks2/DESCR    |  4 ++++
 stacks2/Makefile | 35 ++++++++++++++++++++++++++++++
 stacks2/PLIST    | 66 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 stacks2/distinfo |  6 ++++++
 5 files changed, 113 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 87e3d67490..eee2f7a3a3 100644
--- a/Makefile
+++ b/Makefile
@@ -4345,6 +4345,7 @@ SUBDIR+=	slideml
 SUBDIR+=	slime
 SUBDIR+=	slowhttptest
 SUBDIR+=	slune
+SUBDIR+=	slurm-wlm
 SUBDIR+=	sm-change_ldappass
 SUBDIR+=	sm-change_qldforward
 SUBDIR+=	sm-compatibility
@@ -4407,6 +4408,7 @@ SUBDIR+=	ssid
 SUBDIR+=	ssu
 SUBDIR+=	st-term-git
 SUBDIR+=	stacks
+SUBDIR+=	stacks2
 SUBDIR+=	stardict
 SUBDIR+=	stardict-tools
 SUBDIR+=	starfighter
diff --git a/stacks2/DESCR b/stacks2/DESCR
new file mode 100644
index 0000000000..91c14fbc8d
--- /dev/null
+++ b/stacks2/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/stacks2/Makefile b/stacks2/Makefile
new file mode 100644
index 0000000000..ab9388c18a
--- /dev/null
+++ b/stacks2/Makefile
@@ -0,0 +1,35 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Thu Dec  6 20:39:20 CST 2018               #
+###########################################################
+
+DISTNAME=	stacks-${PV}
+CATEGORIES=	biology
+MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+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++
+USE_TOOLS+=	gmake
+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
+CXXFLAGS=	-fopenmp
+FFLAGS=		-fopenmp
+
+PV=		2.2
+
+# Based on USES=python.  Check this.
+.include "../../lang/python/application.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/stacks2/PLIST b/stacks2/PLIST
new file mode 100644
index 0000000000..9fa33e1618
--- /dev/null
+++ b/stacks2/PLIST
@@ -0,0 +1,66 @@
+@comment $NetBSD$
+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/stacks2/distinfo b/stacks2/distinfo
new file mode 100644
index 0000000000..e62884b666
--- /dev/null
+++ b/stacks2/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+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