stacks: Upgrade to latest available release

[root <root%centosdev.ceas.uwm.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	root <root%centosdev.ceas.uwm.edu@localhost>
Pushed By:	outpaddling
Date:		Thu Mar 22 16:32:12 2018 -0500
Changeset:	6dbecbf608912358be5b066215af68ab6ce5153f

Modified Files:
	stacks/DESCR
	stacks/Makefile
	stacks/PLIST
	stacks/distinfo
Removed Files:
	stacks/TODO

Log Message:
stacks: Upgrade to latest available release

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=6dbecbf608912358be5b066215af68ab6ce5153f

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

diffstat:
 stacks/DESCR    | 10 ++++------
 stacks/Makefile | 11 +++++++----
 stacks/PLIST    | 11 +++++++++--
 stacks/TODO     |  1 -
 stacks/distinfo |  9 +++++----
 5 files changed, 25 insertions(+), 17 deletions(-)

diffs:
diff --git a/stacks/DESCR b/stacks/DESCR
index 9f1e737758..91c14fbc8d 100644
--- a/stacks/DESCR
+++ b/stacks/DESCR
@@ -1,6 +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.
+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
index 6b78ab27da..ab2093af74 100644
--- a/stacks/Makefile
+++ b/stacks/Makefile
@@ -1,24 +1,27 @@
 # $NetBSD$
 #
 ###########################################################
-#               Generated by fbsd2pkg                     #
+#                  Generated by fbsd2pkg                  #
+#              Mon Mar 12 13:58:28 CDT 2018               #
 ###########################################################
 
 DISTNAME=	stacks-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
 
-MAINTAINER=	bacon%NetBSD.org@localhost
+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=	1.35
+PORTVERSION=	1.48
 
+.include "../../lang/python/application.mk"
 .include "../../devel/zlib/buildlink3.mk"
-.include "../../devel/boost-headers/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/stacks/PLIST b/stacks/PLIST
index da2459ea72..e3b8b940cc 100644
--- a/stacks/PLIST
+++ b/stacks/PLIST
@@ -1,13 +1,13 @@
 @comment $NetBSD$
 bin/clone_filter
+bin/count_fixed_catalog_snps.py
 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/integrate_alignments.py
 bin/kmer_filter
 bin/load_radtags.pl
 bin/load_sequences.pl
@@ -59,6 +59,7 @@ 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
@@ -67,3 +68,9 @@ 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/TODO b/stacks/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/stacks/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/stacks/distinfo b/stacks/distinfo
index cb942ba1e2..7e9a7f9ac5 100644
--- a/stacks/distinfo
+++ b/stacks/distinfo
@@ -1,6 +1,7 @@
 $NetBSD$
 
-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
+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