Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 397317) +++ head/biology/Makefile (revision 397318) @@ -1,96 +1,97 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bcftools SUBDIR += biococoa SUBDIR += biojava SUBDIR += blat + SUBDIR += cd-hit SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib SUBDIR += jalview SUBDIR += lagan SUBDIR += lamarc SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += njplot SUBDIR += ortep3 SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-bioperl SUBDIR += p5-bioperl-run SUBDIR += paml SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += platon SUBDIR += plink SUBDIR += plinkseq SUBDIR += povchem SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biopython SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += treeviewx SUBDIR += ugene SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/cd-hit/Makefile =================================================================== --- head/biology/cd-hit/Makefile (nonexistent) +++ head/biology/cd-hit/Makefile (revision 397318) @@ -0,0 +1,41 @@ +# Created by: Jason Bacon +# $FreeBSD$ + +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 Property changes on: head/biology/cd-hit/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/cd-hit/distinfo =================================================================== --- head/biology/cd-hit/distinfo (nonexistent) +++ head/biology/cd-hit/distinfo (revision 397318) @@ -0,0 +1,2 @@ +SHA256 (weizhongli-cdhit-V4.6.4_GH0.tar.gz) = b170108147ec91d8b5f9d10b9e8d5fd971e7aef3af6ec1e5542cbaf10d54b2fc +SIZE (weizhongli-cdhit-V4.6.4_GH0.tar.gz) = 1148426 Property changes on: head/biology/cd-hit/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/cd-hit/pkg-descr =================================================================== --- head/biology/cd-hit/pkg-descr (nonexistent) +++ head/biology/cd-hit/pkg-descr (revision 397318) @@ -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/ Property changes on: head/biology/cd-hit/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/cd-hit/pkg-plist =================================================================== --- head/biology/cd-hit/pkg-plist (nonexistent) +++ head/biology/cd-hit/pkg-plist (revision 397318) @@ -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 Property changes on: head/biology/cd-hit/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property