stacks: 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 Mar 17 13:12:49 2022 -0500
Changeset:	80282878c1e7074d729d58aa43c7fc696c433460

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

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

Working on update to 2.60 and fix for Darwin

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=80282878c1e7074d729d58aa43c7fc696c433460

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

diffstat:
 Makefile        |  1 +
 stacks/DESCR    |  4 ++++
 stacks/Makefile | 38 ++++++++++++++++++++++++++++++++++++++
 stacks/PLIST    | 20 ++++++++++++++++++++
 stacks/distinfo |  5 +++++
 5 files changed, 68 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 778e31ac43..a46acc5a92 100644
--- a/Makefile
+++ b/Makefile
@@ -5354,6 +5354,7 @@ SUBDIR+=	ssid
 SUBDIR+=	ssu
 SUBDIR+=	st-term-git
 SUBDIR+=	stackdriver-collectd
+SUBDIR+=	stacks
 SUBDIR+=	stardict
 SUBDIR+=	stardict-tools
 SUBDIR+=	starfighter
diff --git a/stacks/DESCR b/stacks/DESCR
new file mode 100644
index 0000000000..91c14fbc8d
--- /dev/null
+++ b/stacks/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/stacks/Makefile b/stacks/Makefile
new file mode 100644
index 0000000000..4503f971a7
--- /dev/null
+++ b/stacks/Makefile
@@ -0,0 +1,38 @@
+# $NetBSD: Makefile,v 1.6 2021/05/24 19:49:12 wiz Exp $
+
+DISTNAME=	stacks-2.60
+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
+USE_TOOLS+=	bash perl:run
+GNU_CONFIGURE=	yes
+
+REPLACE_BASH+=		scripts/stacks-count-reads-per-sample-per-locus
+REPLACE_BASH+=		scripts/stacks-dist-extract
+REPLACE_BASH+=		scripts/stacks-gdb
+REPLACE_BASH+=		scripts/stacks-samtools-tview
+REPLACE_PERL=		scripts/*.pl
+REPLACE_PYTHON+=	scripts/*.py
+REPLACE_PYTHON+=	scripts/stacks-integrate-alignments
+
+REPLACE_INTERPRETER+=	Rscript
+REPLACE.Rscript.old=	.*Rscript
+REPLACE.Rscript.new=	${PREFIX}/bin/Rscript
+REPLACE_FILES.Rscript=	scripts/stacks-hist2d-loci-samples-coverage
+
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} != Darwin
+CFLAGS+=	-fopenmp
+.endif
+
+.include "../../lang/python/application.mk"
+.include "../../math/R/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/stacks/PLIST b/stacks/PLIST
new file mode 100644
index 0000000000..2d42a3ee72
--- /dev/null
+++ b/stacks/PLIST
@@ -0,0 +1,20 @@
+@comment $NetBSD$
+bin/clone_filter
+bin/cstacks
+bin/denovo_map.pl
+bin/gstacks
+bin/kmer_filter
+bin/phasedstacks
+bin/populations
+bin/process_radtags
+bin/process_shortreads
+bin/ref_map.pl
+bin/sstacks
+bin/stacks-count-reads-per-sample-per-locus
+bin/stacks-dist-extract
+bin/stacks-gdb
+bin/stacks-hist2d-loci-samples-coverage
+bin/stacks-integrate-alignments
+bin/stacks-samtools-tview
+bin/tsv2bam
+bin/ustacks
diff --git a/stacks/distinfo b/stacks/distinfo
new file mode 100644
index 0000000000..df0955dfd3
--- /dev/null
+++ b/stacks/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+BLAKE2s (stacks-2.60.tar.gz) = 10dc694d464172fdfadec6dadd973d5e44bba83150d564e964479166f87192a5
+SHA512 (stacks-2.60.tar.gz) = 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32
+Size (stacks-2.60.tar.gz) = 12135281 bytes