[pkgsrc/trunk]: pkgsrc/biology/cdhit biology/cdhit: Update to 4.8.1

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/daf78f6b25e2
branches:  trunk
changeset: 771360:daf78f6b25e2
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Fri Dec 17 17:57:55 2021 +0000

description:
biology/cdhit: Update to 4.8.1

Add support for gzipped input

Changes: https://github.com/weizhongli/cdhit/releases

diffstat:

 biology/cdhit/Makefile |  20 +++++++++++---------
 biology/cdhit/PLIST    |   6 +++++-
 biology/cdhit/distinfo |   8 ++++----
 3 files changed, 20 insertions(+), 14 deletions(-)

diffs (84 lines):

diff -r 494e58206560 -r daf78f6b25e2 biology/cdhit/Makefile
--- a/biology/cdhit/Makefile    Fri Dec 17 17:12:40 2021 +0000
+++ b/biology/cdhit/Makefile    Fri Dec 17 17:57:55 2021 +0000
@@ -1,11 +1,6 @@
-# $NetBSD: Makefile,v 1.8 2021/05/24 19:49:10 wiz Exp $
-#
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
+# $NetBSD: Makefile,v 1.9 2021/12/17 17:57:55 bacon Exp $
 
-DISTNAME=      cdhit-4.6.4
-PKGREVISION=   5
+DISTNAME=      cdhit-4.8.1
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=weizhongli/}
 GITHUB_TAG=    V${PKGVERSION_NOREV}
@@ -26,7 +21,7 @@
 SUBST_STAGE.compiler=  pre-configure
 SUBST_MESSAGE.compiler=        Fixing hardcoded compiler name
 SUBST_FILES.compiler=  ${MAKE_FILE}
-SUBST_SED.compiler=    -e 's|g++|${CXX:Q}|g'
+SUBST_SED.compiler=    -e 's|g++|'${CXX:Q}'|g'
 
 SUBST_CLASSES+=                bash
 SUBST_STAGE.bash=      pre-configure
@@ -34,7 +29,13 @@
 SUBST_FILES.bash=      cd-hit-2d-para.pl cd-hit-para.pl
 SUBST_SED.bash=                -e 's|/bin/bash|${PREFIX}/bin/bash|g'
 
-MAKE_FLAGS+=           openmp=yes PREFIX=${DESTDIR}${PREFIX}/bin
+MAKE_FLAGS+=           PREFIX=${DESTDIR}${PREFIX}/bin
+
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == "Darwin"
+MAKE_FLAGS+=           openmp=no
+.endif
 
 DOCDIR=                        ${PREFIX}/share/doc/cdhit
 INSTALLATION_DIRS+=    bin ${DOCDIR}
@@ -42,4 +43,5 @@
 post-install:
        ${INSTALL_DATA} ${WRKSRC}/doc/cdhit-user-guide.pdf ${DESTDIR}${DOCDIR}
 
+.include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff -r 494e58206560 -r daf78f6b25e2 biology/cdhit/PLIST
--- a/biology/cdhit/PLIST       Fri Dec 17 17:12:40 2021 +0000
+++ b/biology/cdhit/PLIST       Fri Dec 17 17:57:55 2021 +0000
@@ -1,8 +1,10 @@
-@comment $NetBSD: PLIST,v 1.1 2015/10/12 16:48:08 leot Exp $
+@comment $NetBSD: PLIST,v 1.2 2021/12/17 17:57:55 bacon Exp $
+bin/FET.pl
 bin/cd-hit
 bin/cd-hit-2d
 bin/cd-hit-2d-para.pl
 bin/cd-hit-454
+bin/cd-hit-clstr_2_blm8.pl
 bin/cd-hit-div
 bin/cd-hit-div.pl
 bin/cd-hit-est
@@ -12,6 +14,8 @@
 bin/clstr2txt.pl
 bin/clstr2xml.pl
 bin/clstr_cut.pl
+bin/clstr_list.pl
+bin/clstr_list_sort.pl
 bin/clstr_merge.pl
 bin/clstr_merge_noorder.pl
 bin/clstr_quality_eval.pl
diff -r 494e58206560 -r daf78f6b25e2 biology/cdhit/distinfo
--- a/biology/cdhit/distinfo    Fri Dec 17 17:12:40 2021 +0000
+++ b/biology/cdhit/distinfo    Fri Dec 17 17:57:55 2021 +0000
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.4 2021/10/26 10:03:38 nia Exp $
+$NetBSD: distinfo,v 1.5 2021/12/17 17:57:55 bacon Exp $
 
-BLAKE2s (cdhit-4.6.4.tar.gz) = bb6cdf9becde665d460c96beaa44f23c617c606e133a4094b162335bb57bf35a
-SHA512 (cdhit-4.6.4.tar.gz) = 01e4de21643667d943055a8dd3447610a57d6e0aac2f7a8133543c5d2c50b60e3a164accaf3131770b679553ec3c6863bd20ae2a57870de142282311b46c567d
-Size (cdhit-4.6.4.tar.gz) = 1148426 bytes
+BLAKE2s (cdhit-4.8.1.tar.gz) = 3660fc912a66ed9ce75ea07c913271e3a63b8e4050a2c26e9a99ba4e4ff919be
+SHA512 (cdhit-4.8.1.tar.gz) = 28f350c67079f000b4102126a29d2eed110c636fb32a8a53699b60e6f3447348ea3838fe87a4dd952895d62491298394a314254e91036f6a23b1956b1e237a64
+Size (cdhit-4.8.1.tar.gz) = 945639 bytes