Fri Dec 17 17:57:55 2021 UTC ()
biology/cdhit: Update to 4.8.1

Add support for gzipped input

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


(bacon)
diff -r1.8 -r1.9 pkgsrc/biology/cdhit/Makefile
diff -r1.1 -r1.2 pkgsrc/biology/cdhit/PLIST
diff -r1.4 -r1.5 pkgsrc/biology/cdhit/distinfo
cvs diff -r1.8 -r1.9 pkgsrc/biology/cdhit/Makefile (expand / switch to unified diff)

--- pkgsrc/biology/cdhit/Makefile 2021/05/24 19:49:10 1.8
+++ pkgsrc/biology/cdhit/Makefile 2021/12/17 17:57:55 1.9
@@ -1,45 +1,47 @@ @@ -1,45 +1,47 @@
1# $NetBSD: Makefile,v 1.8 2021/05/24 19:49:10 wiz Exp $ 1# $NetBSD: Makefile,v 1.9 2021/12/17 17:57:55 bacon Exp $
2# 
3########################################################### 
4# Generated by fbsd2pkg # 
5########################################################### 
6 2
7DISTNAME= cdhit-4.6.4 3DISTNAME= cdhit-4.8.1
8PKGREVISION= 5 
9CATEGORIES= biology 4CATEGORIES= biology
10MASTER_SITES= ${MASTER_SITE_GITHUB:=weizhongli/} 5MASTER_SITES= ${MASTER_SITE_GITHUB:=weizhongli/}
11GITHUB_TAG= V${PKGVERSION_NOREV} 6GITHUB_TAG= V${PKGVERSION_NOREV}
12 7
13MAINTAINER= bacon@NetBSD.org 8MAINTAINER= bacon@NetBSD.org
14HOMEPAGE= http://weizhong-lab.ucsd.edu/cd-hit/ 9HOMEPAGE= http://weizhong-lab.ucsd.edu/cd-hit/
15COMMENT= Clustering and comparing protein or nucleotide sequences 10COMMENT= Clustering and comparing protein or nucleotide sequences
16LICENSE= gnu-gpl-v2 11LICENSE= gnu-gpl-v2
17 12
18USE_LANGUAGES= c++ 13USE_LANGUAGES= c++
19USE_TOOLS+= bash:run gmake perl 14USE_TOOLS+= bash:run gmake perl
20REPLACE_PERL= *.pl 15REPLACE_PERL= *.pl
21 16
22# Restore default overridden by GITHUB_TAG 17# Restore default overridden by GITHUB_TAG
23WRKSRC= ${WRKDIR}/${DISTNAME} 18WRKSRC= ${WRKDIR}/${DISTNAME}
24 19
25SUBST_CLASSES+= compiler 20SUBST_CLASSES+= compiler
26SUBST_STAGE.compiler= pre-configure 21SUBST_STAGE.compiler= pre-configure
27SUBST_MESSAGE.compiler= Fixing hardcoded compiler name 22SUBST_MESSAGE.compiler= Fixing hardcoded compiler name
28SUBST_FILES.compiler= ${MAKE_FILE} 23SUBST_FILES.compiler= ${MAKE_FILE}
29SUBST_SED.compiler= -e 's|g++|${CXX:Q}|g' 24SUBST_SED.compiler= -e 's|g++|'${CXX:Q}'|g'
30 25
31SUBST_CLASSES+= bash 26SUBST_CLASSES+= bash
32SUBST_STAGE.bash= pre-configure 27SUBST_STAGE.bash= pre-configure
33SUBST_MESSAGE.bash= Fixing bash path 28SUBST_MESSAGE.bash= Fixing bash path
34SUBST_FILES.bash= cd-hit-2d-para.pl cd-hit-para.pl 29SUBST_FILES.bash= cd-hit-2d-para.pl cd-hit-para.pl
35SUBST_SED.bash= -e 's|/bin/bash|${PREFIX}/bin/bash|g' 30SUBST_SED.bash= -e 's|/bin/bash|${PREFIX}/bin/bash|g'
36 31
37MAKE_FLAGS+= openmp=yes PREFIX=${DESTDIR}${PREFIX}/bin 32MAKE_FLAGS+= PREFIX=${DESTDIR}${PREFIX}/bin
 33
 34.include "../../mk/bsd.prefs.mk"
 35
 36.if ${OPSYS} == "Darwin"
 37MAKE_FLAGS+= openmp=no
 38.endif
38 39
39DOCDIR= ${PREFIX}/share/doc/cdhit 40DOCDIR= ${PREFIX}/share/doc/cdhit
40INSTALLATION_DIRS+= bin ${DOCDIR} 41INSTALLATION_DIRS+= bin ${DOCDIR}
41 42
42post-install: 43post-install:
43 ${INSTALL_DATA} ${WRKSRC}/doc/cdhit-user-guide.pdf ${DESTDIR}${DOCDIR} 44 ${INSTALL_DATA} ${WRKSRC}/doc/cdhit-user-guide.pdf ${DESTDIR}${DOCDIR}
44 45
 46.include "../../devel/zlib/buildlink3.mk"
45.include "../../mk/bsd.pkg.mk" 47.include "../../mk/bsd.pkg.mk"
cvs diff -r1.1 -r1.2 pkgsrc/biology/cdhit/PLIST (expand / switch to unified diff)

--- pkgsrc/biology/cdhit/PLIST 2015/10/12 16:48:08 1.1
+++ pkgsrc/biology/cdhit/PLIST 2021/12/17 17:57:55 1.2
@@ -1,27 +1,31 @@ @@ -1,27 +1,31 @@
1@comment $NetBSD: PLIST,v 1.1 2015/10/12 16:48:08 leot Exp $ 1@comment $NetBSD: PLIST,v 1.2 2021/12/17 17:57:55 bacon Exp $
 2bin/FET.pl
2bin/cd-hit 3bin/cd-hit
3bin/cd-hit-2d 4bin/cd-hit-2d
4bin/cd-hit-2d-para.pl 5bin/cd-hit-2d-para.pl
5bin/cd-hit-454 6bin/cd-hit-454
 7bin/cd-hit-clstr_2_blm8.pl
6bin/cd-hit-div 8bin/cd-hit-div
7bin/cd-hit-div.pl 9bin/cd-hit-div.pl
8bin/cd-hit-est 10bin/cd-hit-est
9bin/cd-hit-est-2d 11bin/cd-hit-est-2d
10bin/cd-hit-para.pl 12bin/cd-hit-para.pl
11bin/clstr2tree.pl 13bin/clstr2tree.pl
12bin/clstr2txt.pl 14bin/clstr2txt.pl
13bin/clstr2xml.pl 15bin/clstr2xml.pl
14bin/clstr_cut.pl 16bin/clstr_cut.pl
 17bin/clstr_list.pl
 18bin/clstr_list_sort.pl
15bin/clstr_merge.pl 19bin/clstr_merge.pl
16bin/clstr_merge_noorder.pl 20bin/clstr_merge_noorder.pl
17bin/clstr_quality_eval.pl 21bin/clstr_quality_eval.pl
18bin/clstr_quality_eval_by_link.pl 22bin/clstr_quality_eval_by_link.pl
19bin/clstr_reduce.pl 23bin/clstr_reduce.pl
20bin/clstr_renumber.pl 24bin/clstr_renumber.pl
21bin/clstr_rep.pl 25bin/clstr_rep.pl
22bin/clstr_reps_faa_rev.pl 26bin/clstr_reps_faa_rev.pl
23bin/clstr_rev.pl 27bin/clstr_rev.pl
24bin/clstr_select.pl 28bin/clstr_select.pl
25bin/clstr_select_rep.pl 29bin/clstr_select_rep.pl
26bin/clstr_size_histogram.pl 30bin/clstr_size_histogram.pl
27bin/clstr_size_stat.pl 31bin/clstr_size_stat.pl
cvs diff -r1.4 -r1.5 pkgsrc/biology/cdhit/distinfo (expand / switch to unified diff)

--- pkgsrc/biology/cdhit/distinfo 2021/10/26 10:03:38 1.4
+++ pkgsrc/biology/cdhit/distinfo 2021/12/17 17:57:55 1.5
@@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
1$NetBSD: distinfo,v 1.4 2021/10/26 10:03:38 nia Exp $ 1$NetBSD: distinfo,v 1.5 2021/12/17 17:57:55 bacon Exp $
2 2
3BLAKE2s (cdhit-4.6.4.tar.gz) = bb6cdf9becde665d460c96beaa44f23c617c606e133a4094b162335bb57bf35a 3BLAKE2s (cdhit-4.8.1.tar.gz) = 3660fc912a66ed9ce75ea07c913271e3a63b8e4050a2c26e9a99ba4e4ff919be
4SHA512 (cdhit-4.6.4.tar.gz) = 01e4de21643667d943055a8dd3447610a57d6e0aac2f7a8133543c5d2c50b60e3a164accaf3131770b679553ec3c6863bd20ae2a57870de142282311b46c567d 4SHA512 (cdhit-4.8.1.tar.gz) = 28f350c67079f000b4102126a29d2eed110c636fb32a8a53699b60e6f3447348ea3838fe87a4dd952895d62491298394a314254e91036f6a23b1956b1e237a64
5Size (cdhit-4.6.4.tar.gz) = 1148426 bytes 5Size (cdhit-4.8.1.tar.gz) = 945639 bytes