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ORCA

genOmics Research Container Architecture

ORCA is a platform for bioinformatics analysis. It is suited for those wishing to conduct self-serve analysis using their own existing data.

ORCA

Overview

ORCA provides access to a menu of validated bioinformatics software and the power to use these inside a secure and private containerized environment. These private containers are backed by larger mounted storage volumes and dedicated compute nodes to ensure sufficient resources for the demanding needs of bioinformatics analysis.

This Phase-1 implementation of ORCA, is ready to process data now. However, this is only the beginning: ORCA phase-2 will grow to include substantially more compute and storage resources, and an even larger library of software. The system will be optimized and enhanced based on the feedback received from users of the Phase-1 platform.

How it works

ORCA users access the environment through SSH via a gateway address. The ORCA platform then directs their connection into their own private container and mounts their dedicated storage volume. Users then have access to a standard shell where they may launch jobs and return to the container over time to check status and retrieve results. Data transfers in and out of ORCA can be via SCP, SFTP, and/or rsync. There are currently no limits for job duration and since idle containers use only negligible resources the available compute resources are maximized to be shared by all users of the platform.

Included Packages

ORCA includes approximately 500 bioinformatics and analysis software applications and libraries. This ever growing list includes:

Standalone Tools

andi fastqc lumpy-sv python3
art fasttree m4 R
artemis fastuniq mafft readline
astral fermi makedepend recon
autoconf fermi2 maker repeatmasker
automake fermikit maq rmblast
bamhash flash masurca rnammer
bam-readcount flex megahit rna-star
bamtools fqzcomp meme ropebwt2
bamutil freec meraculous sailfish
barrnap fsa metaphlan salmon
bcalm gaemr mhap samtools
bcftools gatb minced snpeff
beast glimmerhmm minia spades
bedops gmap-gsnap mitofy spici
bfc gnuplot mlst sqlite
bioawk grabix mrbayes squeezambler
biobloomtools gsl multi-worm-tracke sratoolkit
biointerchange gsl mummer ssake
bipe harfbuzz muscle stacks
bison hisat ncl stringtie
blasr hisat2 newick-utils szip
blast hlaminer nextflow tasr
blat hmmer novoalign tbb
bowtie hmmer2 parallel tbl2asn
bowtie2 htsbox parsnp trf
bwa humann2 pathd8 trimadap
clustal-omega icu4c pathvisio trimal
clustal-w idba pbsuite trimmomatic
cmake igv pcre unzip
curl igvtools pear uproc
cytoscape infernal phipack vague
daligner jellyfish phylip varscan
dazz_db jellyfish-1.1 phylml vcake
diamond jpeg phyutility vcftools
dida kallisto picard-tools velvet
dsk kat pilon velvetoptimiser
emacs kmc pixman viennarna
exonerate last pkg-config vim
fasq-tools libtool poa yaha
fasta lighter prodigal
fastml lua python2.7


Python Modules

HTSeq pip
matplotlib pysam
numpy PyVCF
pandas scipy
pandas virtualenv

Perl Modules

bioperl
cpanm

Libraries

argtable libcurl
boost libdivsufsort
bzip2 libjpeg
fontconfig libpng
freetype libxml2
gobject-introspection ncurses
hdf5 vcflib
htslib xz
lapack zlib

Acknowledgements

ORCA includes the approximately 180 bioinformatics and analysis software applications and libraries available in Homebrew-Science and are installed using the Linuxbrew package manager. 

Accessing ORCA

ORCA is available as part of the GSC Advanced Research Computing Platform and Compute Canada Node. Platform services at the GSC are collaborative and are available and accessible to any and all qualified researchers based on our Terms of Service.

 To request access, additional information or to arrange for a cost quotation or statement of work, please contact:

Diane Miller, Project Manager
Genome Sciences Centre, BC Cancer Agency
Suite 100, 570 West 7th Ave
Vancouver, BC, V5Z 4S6
Email: dmiller@bcgsc.ca
Phone: (604) 707-5808

Page last modified Sep 28, 2017