Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/stacks stacks-1.35 as wip/ stacks.

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 13:28:06 2016 -0500
Changeset:	dcd7c8be048937dab5334387e14ba5e258e76b7d

Added Files:
	stacks/DESCR
	stacks/Makefile
	stacks/PLIST
	stacks/TODO
	stacks/distinfo

Log Message:
Import /home/bacon/Pkgsrc/pkgsrc-2016Q1/wip/stacks
stacks-1.35 as wip/stacks.

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.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=dcd7c8be048937dab5334387e14ba5e258e76b7d

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

diffstat:
 stacks/DESCR    |  6 +++++
 stacks/Makefile | 24 ++++++++++++++++++++
 stacks/PLIST    | 69 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 stacks/TODO     |  1 +
 stacks/distinfo |  6 +++++
 5 files changed, 106 insertions(+)

diffs:
diff --git a/stacks/DESCR b/stacks/DESCR
new file mode 100644
index 0000000..9f1e737
--- /dev/null
+++ b/stacks/DESCR
@@ -0,0 +1,6 @@
+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/stacks/Makefile b/stacks/Makefile
new file mode 100644
index 0000000..aeffaa4
--- /dev/null
+++ b/stacks/Makefile
@@ -0,0 +1,24 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	stacks-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
+
+MAINTAINER=	bacon4000%gmail.com@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++
+GNU_CONFIGURE=	yes
+REPLACE_PERL=	scripts/*.pl
+
+PORTVERSION=	1.35
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/boost-headers/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/stacks/PLIST b/stacks/PLIST
new file mode 100644
index 0000000..c0e8ddf
--- /dev/null
+++ b/stacks/PLIST
@@ -0,0 +1,69 @@
+@comment $NetBSD$
+bin/clone_filter
+bin/cstacks
+bin/denovo_map.pl
+bin/estacks
+bin/exec_velvet.pl
+bin/export_sql.pl
+bin/genotypes
+bin/hstacks
+bin/index_radtags.pl
+bin/kmer_filter
+bin/load_radtags.pl
+bin/load_sequences.pl
+bin/phasedstacks
+bin/populations
+bin/process_radtags
+bin/process_shortreads
+bin/pstacks
+bin/ref_map.pl
+bin/rxstacks
+bin/sort_read_pairs.pl
+bin/sstacks
+bin/stacks_export_notify.pl
+bin/ustacks
+share/stacks/php/ajax.js
+share/stacks/php/annotate.js
+share/stacks/php/annotate_marker.php
+share/stacks/php/CatalogClass.php
+share/stacks/php/catalog_genotypes.php
+share/stacks/php/catalog.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_batch.php
+share/stacks/php/export.js
+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/Locus.php
+share/stacks/php/phist_view.php
+share/stacks/php/population_view.js
+share/stacks/php/pop_view.php
+share/stacks/php/samples.php
+share/stacks/php/sequence_blast.php
+share/stacks/php/stacks.css
+share/stacks/php/stacks_functions.php
+share/stacks/php/stacks.js
+share/stacks/php/stack_view.php
+share/stacks/php/sumstat_view.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
diff --git a/stacks/TODO b/stacks/TODO
new file mode 100644
index 0000000..b687356
--- /dev/null
+++ b/stacks/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/stacks/distinfo b/stacks/distinfo
new file mode 100644
index 0000000..cb942ba
--- /dev/null
+++ b/stacks/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (stacks-1.35.tar.gz) = fd349084067f0d7d3a2980762832e672cac13f62
+RMD160 (stacks-1.35.tar.gz) = a54c2295d063c301019d4e32160201f47cf00c8c
+SHA512 (stacks-1.35.tar.gz) = 5969d4b706d0d0505a18738dadd7ce6c54e82d1153d3d811b4c5fc2c92badc904e9c4f426b433b8ce1ac7b76c3345d4501be0cdfc50b71664414f225288a09a3
+Size (stacks-1.35.tar.gz) = 501227 bytes