stacks2: Remove following commit to biology

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Dec 22 16:14:04 2018 -0600
Changeset:	e6657ec19d03901b98e3b264e69cd2ce03275185

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

Log Message:
stacks2: Remove following commit to biology

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e6657ec19d03901b98e3b264e69cd2ce03275185

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

diffstat:
 Makefile         |  1 -
 stacks2/DESCR    |  4 ----
 stacks2/Makefile | 26 ----------------------
 stacks2/PLIST    | 66 --------------------------------------------------------
 stacks2/distinfo |  6 ------
 5 files changed, 103 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index 0d3122e84e..d6922f9a46 100644
--- a/Makefile
+++ b/Makefile
@@ -4405,7 +4405,6 @@ 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
deleted file mode 100644
index 91c14fbc8d..0000000000
--- a/stacks2/DESCR
+++ /dev/null
@@ -1,4 +0,0 @@
-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
deleted file mode 100644
index 2b4d020478..0000000000
--- a/stacks2/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	stacks-2.2
-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++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/stacks2/PLIST b/stacks2/PLIST
deleted file mode 100644
index 9fa33e1618..0000000000
--- a/stacks2/PLIST
+++ /dev/null
@@ -1,66 +0,0 @@
-@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
deleted file mode 100644
index e62884b666..0000000000
--- a/stacks2/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-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