ddocent: Add python dep

[Jason W Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Apr 15 09:33:57 2018 -0500
Changeset:	5ceb22aa9e6cec9fe40bb82e9f3a94c2e3b10a8a

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

Log Message:
ddocent: Add python dep

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=5ceb22aa9e6cec9fe40bb82e9f3a94c2e3b10a8a

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

diffstat:
 ddocent/Makefile              | 2 ++
 ddocent/distinfo              | 2 +-
 ddocent/patches/patch-dDocent | 9 +++++++++
 3 files changed, 12 insertions(+), 1 deletion(-)

diffs:
diff --git a/ddocent/Makefile b/ddocent/Makefile
index 4da4caa505..0861dee9d0 100644
--- a/ddocent/Makefile
+++ b/ddocent/Makefile
@@ -44,6 +44,7 @@ SUBST_CLASSES+=		prefix
 SUBST_STAGE.prefix=	post-install
 SUBST_SED.prefix+=	-e 's|%%PREFIX%%|${PREFIX}|g'
 SUBST_SED.prefix+=	-e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g'
+SUBST_SED.prefix+=	-e 's|python|${PYTHON_CMD}|g'
 SUBST_FILES.prefix+=	${DESTDIR}${PREFIX}/bin/dDocent
 
 USE_LANGUAGES=	# none
@@ -75,6 +76,7 @@ do-install:
 		${WRKSRC}/scripts/dDocent_filters \
 		${DESTDIR}${PREFIX}/bin
 
+.include "../../lang/python/tool.mk"
 .include "../../wip/vcflib/buildlink3.mk"
 .include "../../wip/bamtools/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/ddocent/distinfo b/ddocent/distinfo
index a2a866e613..7503da456f 100644
--- a/ddocent/distinfo
+++ b/ddocent/distinfo
@@ -4,4 +4,4 @@ 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) = 339a073908c62680c859dc58258ef938469a8d40
+SHA1 (patch-dDocent) = fbb7e5fdb7dbd5121b8ba1394cf324ffa2577778
diff --git a/ddocent/patches/patch-dDocent b/ddocent/patches/patch-dDocent
index 5c51384c26..a4bc2c8ab5 100644
--- a/ddocent/patches/patch-dDocent
+++ b/ddocent/patches/patch-dDocent
@@ -51,6 +51,15 @@ $NetBSD$
  	if [ "$BWAV" -lt "13" ]; then
          	echo "The version of bwa installed in your" '$PATH' "is not optimized for dDocent."
          	echo "Please install at least version 0.7.13"
+@@ -107,7 +111,7 @@ BTC=$( bedtools --version | mawk '{print
+ 		exit 1	
+ 	fi
+ 		
+-if ! awk --version | fgrep -v GNU &>/dev/null; then
++if ! awk --version | fgrep GNU &>/dev/null; then
+          awk=gawk
+     else
+          awk=awk
 @@ -388,10 +392,10 @@ if [ "$SNP" != "no" ]; then
  	}
  	export -f call_genos