ncbi-blast+: Clean up

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Jan 2 17:07:47 2019 -0600
Changeset:	83d6d2d5def914148b2d0a287d16cfa387f37ea8

Modified Files:
	ncbi-blast+/Makefile
	ncbi-blast+/PLIST
	ncbi-blast+/distinfo

Log Message:
ncbi-blast+: Clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=83d6d2d5def914148b2d0a287d16cfa387f37ea8

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

diffstat:
 ncbi-blast+/Makefile | 16 ++++------------
 ncbi-blast+/PLIST    |  1 -
 ncbi-blast+/distinfo |  2 +-
 3 files changed, 5 insertions(+), 14 deletions(-)

diffs:
diff --git a/ncbi-blast+/Makefile b/ncbi-blast+/Makefile
index 3e8bfa7c6f..3517ac0a01 100644
--- a/ncbi-blast+/Makefile
+++ b/ncbi-blast+/Makefile
@@ -1,10 +1,10 @@
 # $NetBSD: Makefile,v 1.4 2018/07/20 03:34:03 ryoon Exp $
 
-DISTNAME=	ncbi-blast-${PV}+-src
-PKGNAME=	ncbi-blast+-${PV}
+DISTNAME=	ncbi-blast-2.8.1+-src
+PKGNAME=	ncbi-blast+-${PKGVERSION_NOREV}
 CATEGORIES=	biology
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
-		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PV}/
+		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	http://blast.ncbi.nlm.nih.gov/
@@ -20,17 +20,11 @@ SUBST_SED.configure+=	-e '/--infodir=DIR/d'
 SUBST_SED.configure+=	-e '/--mandir=DIR/d'
 SUBST_FILES.configure+=	${WRKSRC}/src/build-system/configure
 
-# Can't use a static patch due to RCS tags in the script
-# Allow REPLACE_BASH to determine platform-dependent final path
-SUBST_CLASSES+=		random
-SUBST_STAGE.random=	pre-configure
-SUBST_SED.random=	-e 's|/bin/sh|/usr/bin/env bash|'
-SUBST_FILES.random=	${WRKSRC}/scripts/common/impl/define_random_macros.sh
-
 USE_TOOLS+=	bash gmake
 USE_LANGUAGES=	c c++
 GNU_CONFIGURE=	yes
 REPLACE_BASH=	scripts/common/impl/define_random_macros.sh
+REPLACE_BASH+=	src/app/blast/get_species_taxids.sh
 REPLACE_PERL=	src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
 REPLACE_PYTHON=	src/app/winmasker/windowmasker_2.2.22_adapter.py
 
@@ -50,8 +44,6 @@ WRKSRC=			${WRKDIR}/${DISTNAME}/c++
 CONFIGURE_ENV+=		ac_cv_func_statfs=no
 .endif
 
-PV=	2.8.1
-
 post-install:
 	${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
 	${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so
diff --git a/ncbi-blast+/PLIST b/ncbi-blast+/PLIST
index e421d5bc3a..88ce4111a3 100644
--- a/ncbi-blast+/PLIST
+++ b/ncbi-blast+/PLIST
@@ -4186,4 +4186,3 @@ lib/ncbi-tools++/libxutil-static.a
 lib/ncbi-tools++/libxutil.a
 lib/ncbi-tools++/libxxconnect-static.a
 lib/ncbi-tools++/libxxconnect.a
-@pkgdir include/ncbi-tools++/objtools/data_loaders/genbank/psg
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
index 8695e2816e..a46bb8c1b0 100644
--- a/ncbi-blast+/distinfo
+++ b/ncbi-blast+/distinfo
@@ -5,7 +5,7 @@ RMD160 (ncbi-blast-2.8.1+-src.tar.gz) = ef8df6c4b3cae18b2ab4509af15554ee8d8f9bfd
 SHA512 (ncbi-blast-2.8.1+-src.tar.gz) = 3f408c5f76704183578828df3272bab7d59dd6052364e73e1831cd005b87d87dcc086bb1799b316b09e639e4af0edea6404b93a4b3e3c159d27cef34fff93d6f
 Size (ncbi-blast-2.8.1+-src.tar.gz) = 24973554 bytes
 SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5
-SHA1 (patch-src_algo_blast_core_blast__kappa.c) = bf434d830a6bb7e9089c7ff1870aae0d8c82ce67
+SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 6fcad996b3a8e5b6c2400608bff9de62ebf6927f
 SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
 SHA1 (patch-src_build-system_cmake_cmake-cfg-unix.sh) = 90468f3109800e01fc7351926adb331919a12fb2
 SHA1 (patch-src_build-system_cmake_cmake-configure) = 7b9a10447b1dd665200ee73a2180b3210f586b97