Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 455381) +++ head/biology/Makefile (revision 455382) @@ -1,118 +1,119 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib 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-transdecoder SUBDIR += paml 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-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/kallisto/Makefile =================================================================== --- head/biology/kallisto/Makefile (nonexistent) +++ head/biology/kallisto/Makefile (revision 455382) @@ -0,0 +1,33 @@ +# $FreeBSD$ + +PORTNAME= kallisto +DISTVERSIONPREFIX= v +DISTVERSION= 0.43.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Quantify abundances of transcripts from RNA-Seq data + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/license.txt + +LIB_DEPENDS= libhdf5.so:science/hdf5 \ + libsz.so:science/szip + +USES= cmake +USE_GITHUB= yes +GH_ACCOUNT= pachterlab + +SUB_FILES= kallisto-test + +PORTEXAMPLES= * +PLIST_FILES= bin/kallisto +EXAMPLES_PLIST_FILES= bin/kallisto-test + +OPTIONS_DEFINE= EXAMPLES + +post-install-EXAMPLES-on: + ${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin + cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} + +.include Property changes on: head/biology/kallisto/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/kallisto/distinfo =================================================================== --- head/biology/kallisto/distinfo (nonexistent) +++ head/biology/kallisto/distinfo (revision 455382) @@ -0,0 +1,3 @@ +TIMESTAMP = 1512166931 +SHA256 (pachterlab-kallisto-v0.43.1_GH0.tar.gz) = 2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e +SIZE (pachterlab-kallisto-v0.43.1_GH0.tar.gz) = 1067076 Property changes on: head/biology/kallisto/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/kallisto/files/kallisto-test.in =================================================================== --- head/biology/kallisto/files/kallisto-test.in (nonexistent) +++ head/biology/kallisto/files/kallisto-test.in (revision 455382) @@ -0,0 +1,48 @@ +#!/bin/sh + +########################################################################## +# Script description: +# +# Arguments: +# +# Returns: +# +# History: +# Date Name Modification +# 2016-03-21 Charlie & Begin +########################################################################## + +usage() +{ + printf "Usage: $0 test-directory\n" + exit 1 +} + + +########################################################################## +# Main +########################################################################## + +if [ $# != 1 ]; then + usage +fi + +dir="$1" +if [ -e "$dir" ]; then + printf "$dir already exists. Remove it first or choose a different name.\n" + exit 1 +fi + +cp -iR %%EXAMPLESDIR%% "$dir" +cd "$dir" +kallisto index -i transcripts.idx transcripts.fasta.gz +kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz +ls -l output +more output/abundance.tsv + +cat << EOM + +See https://pachterlab.github.io/kallisto/starting.html for instructions +on interpreting the output above. + +EOM Property changes on: head/biology/kallisto/files/kallisto-test.in ___________________________________________________________________ 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/kallisto/pkg-descr =================================================================== --- head/biology/kallisto/pkg-descr (nonexistent) +++ head/biology/kallisto/pkg-descr (revision 455382) @@ -0,0 +1,6 @@ +Kallisto is a program for quantifying abundances of transcripts from RNA-Seq +data, or more generally of target sequences using high-throughput sequencing +reads. It is based on the novel idea of pseudoalignment for rapidly determining +the compatibility of reads with targets, without the need for alignment. + +WWW: https://pachterlab.github.io/kallisto/about.html Property changes on: head/biology/kallisto/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