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authorbacon <bacon@pkgsrc.org>2021-12-17 17:57:55 +0000
committerbacon <bacon@pkgsrc.org>2021-12-17 17:57:55 +0000
commit4ec36670551f46b00d3bf7d05f26ce305938e335 (patch)
treee9d76fc1722e1f0737588287f928cba1232ac264 /biology
parent5d9bc86651e88b03dd3c0de643e3bc863cc654de (diff)
downloadpkgsrc-4ec36670551f46b00d3bf7d05f26ce305938e335.tar.gz
biology/cdhit: Update to 4.8.1
Add support for gzipped input Changes: https://github.com/weizhongli/cdhit/releases
Diffstat (limited to 'biology')
-rw-r--r--biology/cdhit/Makefile22
-rw-r--r--biology/cdhit/PLIST6
-rw-r--r--biology/cdhit/distinfo8
3 files changed, 21 insertions, 15 deletions
diff --git a/biology/cdhit/Makefile b/biology/cdhit/Makefile
index 329b7e2f149..f1f0d963649 100644
--- a/biology/cdhit/Makefile
+++ b/biology/cdhit/Makefile
@@ -1,11 +1,6 @@
-# $NetBSD: Makefile,v 1.8 2021/05/24 19:49:10 wiz Exp $
-#
-###########################################################
-# Generated by fbsd2pkg #
-###########################################################
-
-DISTNAME= cdhit-4.6.4
-PKGREVISION= 5
+# $NetBSD: Makefile,v 1.9 2021/12/17 17:57:55 bacon Exp $
+
+DISTNAME= cdhit-4.8.1
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=weizhongli/}
GITHUB_TAG= V${PKGVERSION_NOREV}
@@ -26,7 +21,7 @@ SUBST_CLASSES+= compiler
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++|'${CXX:Q}'|g'
SUBST_CLASSES+= bash
SUBST_STAGE.bash= pre-configure
@@ -34,7 +29,13 @@ SUBST_MESSAGE.bash= Fixing bash path
SUBST_FILES.bash= cd-hit-2d-para.pl cd-hit-para.pl
SUBST_SED.bash= -e 's|/bin/bash|${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 @@ INSTALLATION_DIRS+= bin ${DOCDIR}
post-install:
${INSTALL_DATA} ${WRKSRC}/doc/cdhit-user-guide.pdf ${DESTDIR}${DOCDIR}
+.include "../../devel/zlib/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
diff --git a/biology/cdhit/PLIST b/biology/cdhit/PLIST
index 4dc806a7615..66f14b99269 100644
--- a/biology/cdhit/PLIST
+++ b/biology/cdhit/PLIST
@@ -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/clstr2tree.pl
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 --git a/biology/cdhit/distinfo b/biology/cdhit/distinfo
index 85fdef6bc99..9e0375762c9 100644
--- a/biology/cdhit/distinfo
+++ b/biology/cdhit/distinfo
@@ -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