Add bpcscripts: Gast Illumina processing

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Fri Mar 31 08:16:52 2017 -0500
Changeset:	a8766a05b5886a413f5f8a15b476ed87bcf3ce26

Modified Files:
	Makefile
Added Files:
	bpcscripts/DESCR
	bpcscripts/Makefile
	bpcscripts/PLIST
	bpcscripts/TODO
	bpcscripts/distinfo

Log Message:
Add bpcscripts: 	Gast Illumina processing

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a8766a05b5886a413f5f8a15b476ed87bcf3ce26

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

diffstat:
 Makefile            |  1 +
 bpcscripts/DESCR    |  2 ++
 bpcscripts/Makefile | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 bpcscripts/PLIST    |  3 +++
 bpcscripts/TODO     |  1 +
 bpcscripts/distinfo |  6 ++++++
 6 files changed, 59 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 3354cd92ef..6b66b6d975 100644
--- a/Makefile
+++ b/Makefile
@@ -250,6 +250,7 @@ SUBDIR+=	boost-test-suite
 SUBDIR+=	boost-threadpool
 SUBDIR+=	bowtie
 SUBDIR+=	bowtie2
+SUBDIR+=	bpcscripts
 SUBDIR+=	bpmcounter
 SUBDIR+=	breeze
 SUBDIR+=	breeze-gtk
diff --git a/bpcscripts/DESCR b/bpcscripts/DESCR
new file mode 100644
index 0000000000..48e183b730
--- /dev/null
+++ b/bpcscripts/DESCR
@@ -0,0 +1,2 @@
+Global Alignment for Sequence Taxonomy uses a reference database of SSU
+sequences to determine the taxonomy of hypervariable region tags.
diff --git a/bpcscripts/Makefile b/bpcscripts/Makefile
new file mode 100644
index 0000000000..8208e0af26
--- /dev/null
+++ b/bpcscripts/Makefile
@@ -0,0 +1,46 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Fri May 20 17:44:36 CDT 2016               #
+###########################################################
+
+DISTNAME=	bpcscripts-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=MBL-Woods-Hole/}
+GITHUB_PROJECT=	BPC-scripts
+GITHUB_TAG=	73c814a243955dc64ee248d9dacd4f71ac8640dc
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	https://vamps.mbl.edu/resources/software.php
+COMMENT=	Gast Illumina processing
+# Check this
+LICENSE=	mit
+
+USE_LANGUAGES=	# empty
+USE_TOOLS+=	perl:run
+REPLACE_PERL=	gast_ill
+NO_BUILD=	yes
+
+SUBST_CLASSES+=		perllib
+SUBST_STAGE.perllib=	post-patch
+SUBST_SED.perllib=	-e "s|use Taxonomy;|use lib(\"${SITE_PERL}/${PORTNAME}\"); &|g"
+SUBST_FILES.perllib+=	&|g"
+SUBST_FILES.perllib+=	${WRKSRC}/gast_ill
+
+DEPENDS+=	vsearch-[0-9]*:../../wip/vsearch
+DEPENDS+=	fastaunique-[0-9]*:../../wip/fastaunique
+
+PORTNAME=	bpcscripts
+PORTVERSION=	2016.02.09
+SITE_PERL=	${PREFIX}/share
+
+INSTALLATION_DIRS=	bin ${SITE_PERL}/${PORTNAME}
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/gast_ill ${DESTDIR}${PREFIX}/bin
+	${MKDIR} ${DESTDIR}/${SITE_PERL}/${PORTNAME}
+	${INSTALL_DATA} ${WRKSRC}/*.pm \
+		${DESTDIR}${SITE_PERL}/${PORTNAME}
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/bpcscripts/PLIST b/bpcscripts/PLIST
new file mode 100644
index 0000000000..3a9639fed4
--- /dev/null
+++ b/bpcscripts/PLIST
@@ -0,0 +1,3 @@
+@comment $NetBSD$
+bin/gast_ill
+share/bpcscripts/Taxonomy.pm
diff --git a/bpcscripts/TODO b/bpcscripts/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/bpcscripts/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/bpcscripts/distinfo b/bpcscripts/distinfo
new file mode 100644
index 0000000000..a0be309fdb
--- /dev/null
+++ b/bpcscripts/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (bpcscripts-2016.02.09-73c814a243955dc64ee248d9dacd4f71ac8640dc.tar.gz) = 3a966bed72cef5567069dc073c399a55cf811034
+RMD160 (bpcscripts-2016.02.09-73c814a243955dc64ee248d9dacd4f71ac8640dc.tar.gz) = 53b588105cfbc168823b275a4ef1ed81d75b82a7
+SHA512 (bpcscripts-2016.02.09-73c814a243955dc64ee248d9dacd4f71ac8640dc.tar.gz) = cb0c158cbc9952f27781536ce62154d79bb409764d339f256cda854a11c8585e319ac896a748043a25362d64c2da83c0172039e7d0b7d181e90fdf90734c2501
+Size (bpcscripts-2016.02.09-73c814a243955dc64ee248d9dacd4f71ac8640dc.tar.gz) = 9480 bytes