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CD-HIT is a very widely used program for clustering and comparing protein or

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nucleotide sequences.

WWW: http://weizhong-lab.ucsd.edu/cd-hit/

PR:		203183
Submitted by:	jwbacon@tds.net
This commit is contained in:
Wen Heping 2015-09-19 11:16:51 +00:00
parent 84306b8982
commit cd1751b03f
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=397318
5 changed files with 81 additions and 0 deletions
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1
biology/Makefile
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@ -11,6 +11,7 @@
SUBDIR += biococoa
SUBDIR += biojava
SUBDIR += blat
SUBDIR += cd-hit
SUBDIR += chemeq
SUBDIR += clustalw
SUBDIR += consed

41
biology/cd-hit/Makefile Normal file
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@ -0,0 +1,41 @@
# Created by: Jason Bacon <jwbacon@tds.net>
# $FreeBSD$
PORTNAME= cd-hit
PORTVERSION= 4.6.4
DISTVERSIONPREFIX= V
CATEGORIES= biology
MAINTAINER= jwbacon@tds.net
COMMENT= Clustering and comparing protein or nucleotide sequences
LICENSE= GPLv2
USE_GITHUB= yes
GH_ACCOUNT= weizhongli
GH_PROJECT= cdhit
USES= gmake shebangfix
WRKSRC= ${WRKDIR}/cdhit-${PORTVERSION}
# Only for OpenMP
USE_GCC= yes
SHEBANG_FILES= ${WRKSRC}/*.pl
#MAKEFILE= makefile
MAKE_FLAGS= openmp=yes
post-patch:
@${REINPLACE_CMD} \
-e 's|g++|${CXX}|g' \
-e 's|\$$(PREFIX)|$${DESTDIR}$${PREFIX}/bin|g' \
${WRKSRC}/${MAKEFILE}
@${REINPLACE_CMD} \
-e 's|/bin/bash|${LOCALBASE}/bin/bash|g' \
${WRKSRC}/*.pl
post-stage:
@cd ${STAGEDIR}${PREFIX}/bin && \
${STRIP_CMD} cd-hit cd-hit-2d cd-hit-454 \
cd-hit-div cd-hit-est cd-hit-est-2d
.include <bsd.port.mk>

2
biology/cd-hit/distinfo Normal file
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@ -0,0 +1,2 @@
SHA256 (weizhongli-cdhit-V4.6.4_GH0.tar.gz) = b170108147ec91d8b5f9d10b9e8d5fd971e7aef3af6ec1e5542cbaf10d54b2fc
SIZE (weizhongli-cdhit-V4.6.4_GH0.tar.gz) = 1148426

4
biology/cd-hit/pkg-descr Normal file
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@ -0,0 +1,4 @@
CD-HIT is a very widely used program for clustering and comparing protein or
nucleotide sequences.
WWW: http://weizhong-lab.ucsd.edu/cd-hit/

33
biology/cd-hit/pkg-plist Normal file
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@ -0,0 +1,33 @@
bin/cd-hit
bin/cd-hit-2d
bin/cd-hit-2d-para.pl
bin/cd-hit-454
bin/cd-hit-div
bin/cd-hit-div.pl
bin/cd-hit-est
bin/cd-hit-est-2d
bin/cd-hit-para.pl
bin/clstr2tree.pl
bin/clstr2txt.pl
bin/clstr2xml.pl
bin/clstr_cut.pl
bin/clstr_merge.pl
bin/clstr_merge_noorder.pl
bin/clstr_quality_eval.pl
bin/clstr_quality_eval_by_link.pl
bin/clstr_reduce.pl
bin/clstr_renumber.pl
bin/clstr_rep.pl
bin/clstr_reps_faa_rev.pl
bin/clstr_rev.pl
bin/clstr_select.pl
bin/clstr_select_rep.pl
bin/clstr_size_histogram.pl
bin/clstr_size_stat.pl
bin/clstr_sort_by.pl
bin/clstr_sort_prot_by.pl
bin/clstr_sql_tbl.pl
bin/clstr_sql_tbl_sort.pl
bin/make_multi_seq.pl
bin/plot_2d.pl
bin/plot_len1.pl