Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 471849) +++ head/biology/Makefile (revision 471850) @@ -1,141 +1,142 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed SUBDIR += crux SUBDIR += ddocent SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy + SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils 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 += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO 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 += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += ssaha SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += unanimity SUBDIR += vcftools SUBDIR += vcflib SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/infernal/Makefile =================================================================== --- head/biology/infernal/Makefile (nonexistent) +++ head/biology/infernal/Makefile (revision 471850) @@ -0,0 +1,46 @@ +# $FreeBSD$ + +PORTNAME= infernal +PORTVERSION= 1.1.2 +CATEGORIES= biology +MASTER_SITES= http://eddylab.org/infernal/ + +MAINTAINER= mzaki@niid.go.jp +COMMENT= Search sequence databases for structural RNA homologs + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +ONLY_FOR_ARCHS= amd64 i386 +ONLY_FOR_ARCHS_REASON= requires SSE2 or AltiVec instructions + +USES= gmake +GNU_CONFIGURE= yes +MAKE_ARGS= V=1 + +DOCFILES= Userguide.pdf +EXAMPLES= 5S_rRNA.c.cm 5S_rRNA.sto \ + Cobalamin.c.cm Cobalamin.fa Cobalamin.sto \ + metag-example.fa minifam-metag.out minifam.cm \ + minifam.cm.i1f minifam.cm.i1i minifam.cm.i1m minifam.cm.i1p \ + mrum-genome.fa mrum-tRNAs10.fa mrum-tRNAs10.out \ + tRNA5-hand.c.cm tRNA5-hand.sto tRNA5-mrum.out \ + tRNA5-noss.sto tRNA5.c.cm tRNA5.sto + +OPTIONS_DEFINE= DOCS EXAMPLES TEST + +TEST_TEST_TARGET= check +TEST_USES= shebangfix perl5 +TEST_VARS= shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build + +post-build-TEST-on: do-test + +post-install-DOCS-on: + @${MKDIR} ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR} + +post-install-EXAMPLES-on: + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + ${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR} + +.include Property changes on: head/biology/infernal/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/infernal/distinfo =================================================================== --- head/biology/infernal/distinfo (nonexistent) +++ head/biology/infernal/distinfo (revision 471850) @@ -0,0 +1,3 @@ +TIMESTAMP = 1528251928 +SHA256 (infernal-1.1.2.tar.gz) = ac8c24f484205cfb7124c38d6dc638a28f2b9035b9433efec5dc753c7e84226b +SIZE (infernal-1.1.2.tar.gz) = 19364073 Property changes on: head/biology/infernal/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/infernal/files/patch-configure =================================================================== --- head/biology/infernal/files/patch-configure (nonexistent) +++ head/biology/infernal/files/patch-configure (revision 471850) @@ -0,0 +1,10 @@ +--- configure.orig 2016-07-01 20:26:34 UTC ++++ configure +@@ -3855,6 +3855,7 @@ fi + if test "$impl_choice" = "none"; then + case $host in + ia64-*-*) impl_choice=sse;; ++ amd64-*-*) impl_choice=sse;; + i?86-*-*) impl_choice=sse;; + x86*-*-*) impl_choice=sse;; + powerpc*-*-*) impl_choice=vmx;; Property changes on: head/biology/infernal/files/patch-configure ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/infernal/pkg-descr =================================================================== --- head/biology/infernal/pkg-descr (nonexistent) +++ head/biology/infernal/pkg-descr (revision 471850) @@ -0,0 +1,14 @@ +Infernal, standing for "INFERence of RNA ALignment", is a tool for searching +DNA sequence database for RNA structure and sequence similarities. + +It is based on Covariance Model (CM), which scores a combination of sequence +consensus and RNA secondary structure consensus, and thus is more capable of +identifying RNA homologs than using primary sequence profile. + +The Rfam database of RNA families is based on Infernal. + +Citation: +Nawrocki & Eddy (2013) Infernal 1.1: 100-fold faster RNA homology searches, +Bioinformatics 29: 2933-2935. + +WWW: http://eddylab.org/infernal/ Property changes on: head/biology/infernal/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/infernal/pkg-plist =================================================================== --- head/biology/infernal/pkg-plist (nonexistent) +++ head/biology/infernal/pkg-plist (revision 471850) @@ -0,0 +1,43 @@ +bin/cmalign +bin/cmbuild +bin/cmcalibrate +bin/cmconvert +bin/cmemit +bin/cmfetch +bin/cmpress +bin/cmscan +bin/cmsearch +bin/cmstat +man/man1/cmalign.1.gz +man/man1/cmbuild.1.gz +man/man1/cmcalibrate.1.gz +man/man1/cmconvert.1.gz +man/man1/cmemit.1.gz +man/man1/cmfetch.1.gz +man/man1/cmpress.1.gz +man/man1/cmscan.1.gz +man/man1/cmsearch.1.gz +man/man1/cmstat.1.gz +man/man1/infernal.1.gz +%%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5S_rRNA.c.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5S_rRNA.sto +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.c.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.fa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Cobalamin.sto +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/metag-example.fa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam-metag.out +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1f +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1i +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1m +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.cm.i1p +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-genome.fa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-tRNAs10.fa +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mrum-tRNAs10.out +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.c.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-hand.sto +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-mrum.out +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5-noss.sto +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5.c.cm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tRNA5.sto Property changes on: head/biology/infernal/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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