Name: manifest-to-consonance
Owner: CancerCollaboratory
Description: A tool that converts from a DCC Portal manifest file to a workflow order in the Consonance system.
Created: 2015-10-27 14:03:13.0
Updated: 2015-10-28 14:54:54.0
Pushed: 2015-11-10 20:40:17.0
Homepage: null
Size: 17338
Language: Perl
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A tool that converts from a DCC Portal manifest file to Docker container runs using tool images from the Dockstore. It can run these Docker containers locally or it can send “orders” to the Consonance system which runs them on fleets of Cloud VMs.
A use case for this tool is to search for a subset of BAM files from the ICGC PanCancer project indexed on the DCC Portal, select those for analysis with a Docker-based analysis tool from the Dockstore, and then to run the analysis on either a commercial/private cloud or on your local machine. In this way you can do large-scale analysis with the ICGC data files.
You can contrinbute your own Docker-based tools to the Dockstore, see http://www.dockstore.org for more details.
This tool supports two modes, a local mode and a Consonance mode. They each have their own depedencies although the following will need to be setup for any type of run:
sudo cpanm install YAML::Perl
sudo apt-get install libjson-pp-perl libconfig-yaml-perl libwww-perl libyaml-perl cpanminus python-pip make libcurl4-openssl-dev python-dev
and the same command above since there is no package for YAML::PerlYou need to have the:
mvn clean install
in the launcher
directorylib
cwltool
command, see here for how to install in detailpip install cwl-runner
You need to have the:
The ICGC PanCancer data is located on AWS (in S3) and the Collaboratory at OICR. A special tool is required in order to download data from these two sources. You need to download the following to the deps directory.
wget -O deps/dcc-storage-client-0.0.43-dist.tar.gz https://seqwaremaven.oicr.on.ca/artifactory/simple/dcc-release/org/icgc/dcc/dcc-storage-client/0.0.43/dcc-storage-client-0.0.43-dist.tar.gz
And then unzip it.You will also fill in the config file for this tool in deps/dcc-storage-client-0.0.43/conf/application-amazon.properties
, make sure you fill
in your token:
ing.level.org.icgc.dcc.storage.client=DEBUG
ing.level.org.springframework.web.client.RestTemplate=DEBUG
nt.upload.serviceHostname=storage.cancercollaboratory.org
nt.ssl.trustStore=classpath:client.jks
ssToken=<your token here>
You then should update the config/launcher.ini
file, correct the path below for your system:
[dcc_storage]
client=<path>/deps/dcc-storage-client-0.0.43/bin/dcc-storage-client
The perl script will execute the various commands in a shell started with bash -l -c '<command>'
.
This means you need to have the following defined in your ~/.bash_profile
file:
rt JAVA_HOME=<path to JDK 1.8>
rt AWS_ACCESS_KEY=<your key>
rt AWS_SECRET_KEY=<your secret key>
The tool is called collab
since it's for the Collaboratory project.
This will run the BAMStats tool on a collection of BAM files available
perl collab --container-id quay.io/briandoconnor/dockstore-tool-bamstats --manifest manifest.tsv --mode local
perl collab --container-id quay.io/briandoconnor/dockstore-tool-bamstats --manifest manifest.tsv --mode consonance