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authorleot <leot@pkgsrc.org>2015-10-12 16:48:08 +0000
committerleot <leot@pkgsrc.org>2015-10-12 16:48:08 +0000
commitbe3c9994d5a7b49d272f20dd48e71cdb646ad24f (patch)
treeb79d4b585bc971c6fce5459d0a943459bc284149 /biology
parent7dc044442d86ae0df3af8b2defd7b294c44c9873 (diff)
downloadpkgsrc-be3c9994d5a7b49d272f20dd48e71cdb646ad24f.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/DESCR2
-rw-r--r--biology/cdhit/Makefile44
-rw-r--r--biology/cdhit/PLIST35
-rw-r--r--biology/cdhit/distinfo5
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