diff options
| author | leot <leot> | 2015-10-12 16:48:08 +0000 |
|---|---|---|
| committer | leot <leot> | 2015-10-12 16:48:08 +0000 |
| commit | eebca9a479bc1a8365529d5eda4f134279a46fa4 (patch) | |
| tree | b79d4b585bc971c6fce5459d0a943459bc284149 /biology | |
| parent | b5ea7a5c4dc55c4765cca5e3e3e372cd3e9465eb (diff) | |
| download | pkgsrc-eebca9a479bc1a8365529d5eda4f134279a46fa4.tar.gz | |
Import biology/cdhit as cdhit-4.6.4.
Packaged in pkgsrc-wip by Jason Bacon.
CD-HIT is a very widely used program for clustering and comparing protein or
nucleotide sequences.
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/cdhit/DESCR | 2 | ||||
| -rw-r--r-- | biology/cdhit/Makefile | 44 | ||||
| -rw-r--r-- | biology/cdhit/PLIST | 35 | ||||
| -rw-r--r-- | biology/cdhit/distinfo | 5 |
4 files changed, 86 insertions, 0 deletions
diff --git a/biology/cdhit/DESCR b/biology/cdhit/DESCR new file mode 100644 index 00000000000..06848d6e151 --- /dev/null +++ b/biology/cdhit/DESCR @@ -0,0 +1,2 @@ +CD-HIT is a very widely used program for clustering and comparing protein or +nucleotide sequences. diff --git a/biology/cdhit/Makefile b/biology/cdhit/Makefile new file mode 100644 index 00000000000..96e7dbf51bb --- /dev/null +++ b/biology/cdhit/Makefile @@ -0,0 +1,44 @@ +# $NetBSD: Makefile,v 1.1 2015/10/12 16:48:08 leot Exp $ +# +########################################################### +# Generated by fbsd2pkg # +########################################################### + +DISTNAME= cdhit-4.6.4 +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_GITHUB:=weizhongli/} +GITHUB_TAG= V${PKGVERSION_NOREV} + +MAINTAINER= jwbacon@tds.net +HOMEPAGE= http://weizhong-lab.ucsd.edu/cd-hit/ +COMMENT= Clustering and comparing protein or nucleotide sequences +LICENSE= gnu-gpl-v2 + +USE_LANGUAGES= c++ +USE_TOOLS+= bash:run gmake perl +REPLACE_PERL= *.pl + +# Restore default overridden by GITHUB_TAG +WRKSRC= ${WRKDIR}/${DISTNAME} + +SUBST_CLASSES+= compiler +SUBST_STAGE.compiler= post-patch +SUBST_MESSAGE.compiler= Fixing hardcoded compiler name +SUBST_FILES.compiler= ${MAKE_FILE} +SUBST_SED.compiler= -e 's|g++|${CXX:Q}|g' + +SUBST_CLASSES+= bash +SUBST_STAGE.bash= post-patch +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 + +DOCDIR= ${PREFIX}/share/doc/cdhit +INSTALLATION_DIRS+= bin ${DOCDIR} + +post-install: + ${INSTALL_DATA} ${WRKSRC}/doc/cdhit-user-guide.pdf ${DESTDIR}${DOCDIR} + +.include "../../mk/bsd.pkg.mk" diff --git a/biology/cdhit/PLIST b/biology/cdhit/PLIST new file mode 100644 index 00000000000..4dc806a7615 --- /dev/null +++ b/biology/cdhit/PLIST @@ -0,0 +1,35 @@ +@comment $NetBSD: PLIST,v 1.1 2015/10/12 16:48:08 leot Exp $ +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 +share/doc/cdhit/cdhit-user-guide.pdf diff --git a/biology/cdhit/distinfo b/biology/cdhit/distinfo new file mode 100644 index 00000000000..3c484bb072c --- /dev/null +++ b/biology/cdhit/distinfo @@ -0,0 +1,5 @@ +$NetBSD: distinfo,v 1.1 2015/10/12 16:48:08 leot Exp $ + +SHA1 (cdhit-4.6.4.tar.gz) = 3606a8200e62ac60c9dd782a57bec426256e6fa8 +RMD160 (cdhit-4.6.4.tar.gz) = a94a29103393dded87000173d8eb4ec1a1e0614f +Size (cdhit-4.6.4.tar.gz) = 1148426 bytes |