Date: Sat, 2 Dec 2017 20:44:28 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r455382 - in head/biology: . kallisto kallisto/files Message-ID: <201712022044.vB2KiS2b051346@repo.freebsd.org>
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Author: jwb Date: Sat Dec 2 20:44:28 2017 New Revision: 455382 URL: https://svnweb.freebsd.org/changeset/ports/455382 Log: [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13328 Added: head/biology/kallisto/ head/biology/kallisto/Makefile (contents, props changed) head/biology/kallisto/distinfo (contents, props changed) head/biology/kallisto/files/ head/biology/kallisto/files/kallisto-test.in (contents, props changed) head/biology/kallisto/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Dec 2 18:12:09 2017 (r455381) +++ head/biology/Makefile Sat Dec 2 20:44:28 2017 (r455382) @@ -41,6 +41,7 @@ SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish + SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils Added: head/biology/kallisto/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/kallisto/Makefile Sat Dec 2 20:44:28 2017 (r455382) @@ -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 <bsd.port.mk> Added: head/biology/kallisto/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/kallisto/distinfo Sat Dec 2 20:44:28 2017 (r455382) @@ -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 Added: head/biology/kallisto/files/kallisto-test.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/kallisto/files/kallisto-test.in Sat Dec 2 20:44:28 2017 (r455382) @@ -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 Added: head/biology/kallisto/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/kallisto/pkg-descr Sat Dec 2 20:44:28 2017 (r455382) @@ -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
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