ddocent: Working build, minus freebayes

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Fri Mar 30 13:46:02 2018 -0500
Changeset:	bd5132fbbbdda8aff3f8c3f3b9ef0b238a4dde5a

Modified Files:
	ddocent/Makefile
	ddocent/PLIST
	ddocent/distinfo
	ddocent/patches/patch-dDocent

Log Message:
ddocent: Working build, minus freebayes

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=bd5132fbbbdda8aff3f8c3f3b9ef0b238a4dde5a

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

diffstat:
 ddocent/Makefile              | 36 ++++++++++++++++--------------------
 ddocent/PLIST                 | 17 +++++++++++++++++
 ddocent/distinfo              |  8 +++++++-
 ddocent/patches/patch-dDocent |  2 ++
 4 files changed, 42 insertions(+), 21 deletions(-)

diffs:
diff --git a/ddocent/Makefile b/ddocent/Makefile
index 0850632447..eef2b69e08 100644
--- a/ddocent/Makefile
+++ b/ddocent/Makefile
@@ -5,24 +5,19 @@
 #              Thu Mar 22 18:28:27 CDT 2018               #
 ###########################################################
 
-PKGNAME=	dDocent-${PORTVERSION}
+DISTNAME=	dDocent-${PORTVERSION}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=jpuritz/}
 GITHUB_PROJECT=	dDocent
 GITHUB_TAG=	v${PORTVERSION}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://ddocent.com
+HOMEPAGE=	http://ddocent.com/
 COMMENT=	Bash pipeline for RAD sequencing
 LICENSE=	mit
 
-# Notes on 2015.11.30 snapshot:
 # bedtools version: https://github.com/jpuritz/dDocent/issues/15
 # New ddocent works with 2.23.0 or >= 2.26.0
-# vcftools 0.1.14 does not report version the same as 0.1.11, so
-# dDocent script fails to recognize it.  Should be easy to patch
-# assuming 0.1.14 is usable.
-# 0.1.15 reports version properly.
 # Do we really need trimadap?  It used to be part of seqtk.
 # ddocent test data do not unpack with FreeBSD 11.1 /usr/bin/unzip
 DEPENDS=	mawk>=0:../../lang/mawk \
@@ -34,51 +29,52 @@ DEPENDS=	mawk>=0:../../lang/mawk \
 		samtools>=1.3:../../wip/samtools \
 		vcftools>=0.1.15:../../wip/vcftools \
 		Trimmomatic>=0:../../wip/trimmomatic \
-		bamtools>=0:../../wip/bamtools \
 		stacks>=0:../../wip/stacks \
 		rainbow>=0:../../wip/rainbow \
 		trimadap>=0:../../wip/trimadap \
 		seqtk>=0:../../wip/seqtk \
 		bedtools2>=2.26.0:../../wip/bedtools2 \
 		pear-merger>=0:../../wip/pear-merger \
-		freebayes:../../wip/freebayes \
-		vcflib>=0:../../wip/vcflib
+
+#		freebayes>=0:../../wip/freebayes
 
 ## These follow patch-dDocent, so don't apply them within the source tree,
 ## or they'll get picked up by patch generators and hard-code PREFIX
 SUBST_CLASSES+=		prefix
 SUBST_STAGE.prefix=	post-install
-SUBST_SED.prefix+=	-i ''
 SUBST_SED.prefix+=	-e 's|%%PREFIX%%|${PREFIX}|g'
 SUBST_SED.prefix+=	-e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g'
 SUBST_FILES.prefix+=	${DESTDIR}${PREFIX}/bin/dDocent
 
-USE_LANGUAGES=	# None
-REPLACE_BASH=	scripts/*.sh scripts/dDocent_filters dDocent
+USE_LANGUAGES=	# none
+REPLACE_BASH=	dDocent *.sh
+REPLACE_BASH+=	scripts/ddocent-test* scripts/*.sh scripts/dDocent_filters
 REPLACE_PERL=	scripts/*.pl
 REPLACE_PYTHON=	scripts/*.py
 NO_BUILD=	yes
 USE_TOOLS=	bash perl unzip
 
+ERROR: [check-interpreter.mk] The interpreter "/usr/bin/env" of "/usr/pkgsrc/wip/ddocent/work/.destdir/usr/pkg/bin/ddocent-test" is not allowed.
+
 PORTVERSION=	2.2.25
 JAVAJARDIR=	${PREFIX}/share/java/classes
 
 INSTALLATION_DIRS=	bin
 
+post-extract:
+	${CP} ${FILESDIR}/ddocent-test ${FILESDIR}/ddocent-test-cleanup \
+		${WRKSRC}/scripts
+
 do-install:
-	${MKDIR} ${DESTDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} \
 		${WRKSRC}/dDocent \
 		${WRKSRC}/*.sh \
-		${FILESDIR}/ddocent-test \
-		${FILESDIR}/ddocent-test-cleanup \
+		${WRKSRC}/scripts/ddocent-test* \
 		${WRKSRC}/scripts/*.sh \
 		${WRKSRC}/scripts/*.pl \
 		${WRKSRC}/scripts/dDocent_filters \
 		${DESTDIR}${PREFIX}/bin
 
-# Convert any _DEPENDS above that have a buildlink3.mk
-# .include "../..///buildlink3.mk"
-# Linux doesn't have zlib in the base, so just in case...
-# .include "../../devel/zlib/buildlink3.mk"
+.include "../../wip/vcflib/buildlink3.mk"
+.include "../../wip/bamtools/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/ddocent/PLIST b/ddocent/PLIST
index 48d96a5493..fa7987a570 100644
--- a/ddocent/PLIST
+++ b/ddocent/PLIST
@@ -1 +1,18 @@
 @comment $NetBSD$
+bin/ErrorCount.sh
+bin/RefMapOpt.sh
+bin/ReferenceOpt.hyb.sh
+bin/ReferenceOpt.sh
+bin/Rename_SequenceFiles.sh
+bin/Rename_for_dDocent.sh
+bin/Rename_for_dDocent_with-INDEX.sh
+bin/dDocent
+bin/dDocent_filters
+bin/dDocent_ngs.sh
+bin/ddocent-test
+bin/ddocent-test-cleanup
+bin/filter_hwe_by_pop.pl
+bin/filter_missing_ind.sh
+bin/pop_missing_filter.sh
+bin/remake_reference.sh
+bin/remove.bad.hap.loci.sh
diff --git a/ddocent/distinfo b/ddocent/distinfo
index 6afd6c110d..4467da2f9b 100644
--- a/ddocent/distinfo
+++ b/ddocent/distinfo
@@ -1 +1,7 @@
-SHA1 (patch-dDocent) = b78a93e5f78b8a6c291244f5290c73372c0aa202
+$NetBSD$
+
+SHA1 (dDocent-2.2.25.tar.gz) = 5bdb9419a7d6770114d1bb363fcf1af07d49190b
+RMD160 (dDocent-2.2.25.tar.gz) = a33107f9d3269f647f9970b0bfcd14e15bca9575
+SHA512 (dDocent-2.2.25.tar.gz) = d7ba86d363b50dba648bb7b26e4e3c0306b3b5735e9cdea95a8d00164e12649781f325ae3fe8fba14ed76fa6478ecdf3263b07002cd8df3067fb0359e657765a
+Size (dDocent-2.2.25.tar.gz) = 336804 bytes
+SHA1 (patch-dDocent) = 9505cfea35854ff83eefe7c16c59a03c362ed6b3
diff --git a/ddocent/patches/patch-dDocent b/ddocent/patches/patch-dDocent
index d1d524d1e1..919767d8b6 100644
--- a/ddocent/patches/patch-dDocent
+++ b/ddocent/patches/patch-dDocent
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Locate tools installed via pkgsrc
+
 --- dDocent.orig	2018-03-06 14:22:03 UTC
 +++ dDocent
 @@ -27,15 +27,15 @@ do