stacks: Remove outdated package, newer version already committed

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: stacks: Remove outdated package, newer version already committed
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Sat, 04 May 2019 16:18:50 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat May 4 11:18:50 2019 -0500
Changeset:	d696d5aa1db07dd5f277c703cd3155b4576843bc

Modified Files:
	Makefile
	ddocent/Makefile
Removed Files:
	stacks/DESCR
	stacks/Makefile
	stacks/PLIST
	stacks/distinfo
	stacks/patches/patch-htslib_Makefile

Log Message:
stacks: Remove outdated package, newer version already committed

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d696d5aa1db07dd5f277c703cd3155b4576843bc

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

diffstat:
 Makefile                             |  1 -
 ddocent/Makefile                     |  2 +-
 stacks/DESCR                         |  4 --
 stacks/Makefile                      | 22 -----------
 stacks/PLIST                         | 76 ------------------------------------
 stacks/distinfo                      |  7 ----
 stacks/patches/patch-htslib_Makefile | 23 -----------
 7 files changed, 1 insertion(+), 134 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index 2fa9d7208a..7bdbfb006d 100644
--- a/Makefile
+++ b/Makefile
@@ -4513,7 +4513,6 @@ SUBDIR+=	ssid
 SUBDIR+=	ssu
 SUBDIR+=	st-term-git
 SUBDIR+=	stackdriver-collectd
-SUBDIR+=	stacks
 SUBDIR+=	stagit
 SUBDIR+=	stardict
 SUBDIR+=	stardict-tools
diff --git a/ddocent/Makefile b/ddocent/Makefile
index b6e9210ac0..10bfcb6f32 100644
--- a/ddocent/Makefile
+++ b/ddocent/Makefile
@@ -30,7 +30,7 @@ DEPENDS=	mawk>=0:../../lang/mawk \
 		samtools>=1.3:../../wip/samtools \
 		vcftools>=0.1.15:../../wip/vcftools \
 		Trimmomatic>=0:../../wip/trimmomatic \
-		stacks>=0:../../wip/stacks \
+		stacks>=0:../../biology/stacks \
 		rainbow>=0:../../wip/rainbow \
 		trimadap>=0:../../wip/trimadap \
 		seqtk>=0:../../wip/seqtk \
diff --git a/stacks/DESCR b/stacks/DESCR
deleted file mode 100644
index 91c14fbc8d..0000000000
--- a/stacks/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/stacks/Makefile b/stacks/Makefile
deleted file mode 100644
index fe8cd94694..0000000000
--- a/stacks/Makefile
+++ /dev/null
@@ -1,22 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	stacks-${PORTVERSION}
-CATEGORIES=	biology
-MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
-
-MAINTAINER=	dsiercks%uwm.edu@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_PERL=	scripts/*.pl
-REPLACE_PYTHON=	scripts/*.py
-
-PORTVERSION=	1.48
-
-.include "../../lang/python/application.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/stacks/PLIST b/stacks/PLIST
deleted file mode 100644
index e3b8b940cc..0000000000
--- a/stacks/PLIST
+++ /dev/null
@@ -1,76 +0,0 @@
-@comment $NetBSD$
-bin/clone_filter
-bin/count_fixed_catalog_snps.py
-bin/cstacks
-bin/denovo_map.pl
-bin/exec_velvet.pl
-bin/export_sql.pl
-bin/genotypes
-bin/index_radtags.pl
-bin/integrate_alignments.py
-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/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
-@pkgdir share/examples
-@pkgdir share/doc
-@pkgdir man/man1
-@pkgdir lib
-@pkgdir include
diff --git a/stacks/distinfo b/stacks/distinfo
deleted file mode 100644
index 7e9a7f9ac5..0000000000
--- a/stacks/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD$
-
-SHA1 (stacks-1.48.tar.gz) = 6959023f5f7073d18b5048e97643aab1ee92d109
-RMD160 (stacks-1.48.tar.gz) = 874de582a5de4bd448575ba230a78b5048577f89
-SHA512 (stacks-1.48.tar.gz) = 792f697fd1e23d7b7a1138af3fc3725705d3930faacd1bc0411e1bdea7254981b2cc369dc824213c15c2c8fad56d7f910c6647e7886252f9b388028d6900b49a
-Size (stacks-1.48.tar.gz) = 895195 bytes
-SHA1 (patch-htslib_Makefile) = 0bceb9bcabb8d328800673588e79d0b2a276ab96
diff --git a/stacks/patches/patch-htslib_Makefile b/stacks/patches/patch-htslib_Makefile
deleted file mode 100644
index 60c36be78c..0000000000
--- a/stacks/patches/patch-htslib_Makefile
+++ /dev/null
@@ -1,23 +0,0 @@
-$NetBSD$
-
-#use pkgsrc defined compiler
---- htslib/Makefile.orig	2016-09-16 15:40:03 UTC
-+++ htslib/Makefile
-@@ -22,13 +22,13 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC     = gcc
--AR     = ar
--RANLIB = ranlib
-+CC     ?= gcc
-+AR     ?= ar
-+RANLIB ?= ranlib
- 
- CPPFLAGS =
- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
--CFLAGS   = -g -Wall -O2
-+CFLAGS   ?= -g -Wall -O2
- EXTRA_CFLAGS_PIC = -fpic
- LDFLAGS  =
- LIBS     =
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