Name: docker-assembly
Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada
Owner: Biological Informatics CoE @ Agriculture and Agri-Food Canada
Description: Assembly pipeline using Docker and SPAdes
Created: 2016-02-02 16:21:36.0
Updated: 2016-03-07 21:31:48.0
Pushed: 2016-11-07 18:42:13.0
Homepage: null
Size: 94
Language: Perl
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|
Other Committers
| User | Most Recent Commit | # Commits |
|---|
These are the instructions to build a docker image containing the blackbox-pipeline.
We packaged accessoryfiles script to create a folder called accessoryfiles in the directory it was run.
At first you need to install docker. Please follow the very good instructions from the Docker project.
After the successful installation, all what you need to do is:
Build the image:
er build -t docker-assembly https://github.com/AAFC-MBB/docker-assembly.git
You may need to download the required packages for the pipeline to run, you will have to specify their location on execution
-fsSL https://raw.githubusercontent.com/AAFC-MBB/docker-assembly/master/accessoryfiles.sh | bash
er run -u $(id -u) -v path/to/fastq/data -v path/to/accessory/files:/accessoryfiles ....
For docker setup using docker-machine with openstack and the ubuntu coud image, the default user is ubuntu with uid = 1000. This will alter thhe above docker run command to the following
er run -u 1000 ...
To use a MiSeq library (fastq files including SampleSheet.csv`GenerateFASTQRunStatistics.xmlRunInfo.xml) stored inside folder labeleddatain the home folder (/home/ubuntu/`) of an OpenStack instance:
First you must download and execute the accessoryfiles script:
To download the requirements to an accessoryfiles folder
-fsSL https://raw.githubusercontent.com/AAFC-MBB/docker-assembly/master/accessoryfiles.sh | bash
docker-machine the command becomeser-machine ssh <machine name> "curl -fsSL https://raw.githubusercontent.com/AAFC-MBB/docker-assembly/master/accessoryfiles.sh | bash"
Where <machine name> is replaced with the name you used to with the docker-machine create command
er run -it -u 1000 -v /home/ubuntu/data:/home/ubuntu/data \
home/ubuntu/accessoryfiles:/accessoryfiles docker-assembly /home/ubuntu/data
The above command can be broken down into:
docker run the command line instruction run a built container-it flag for both interactive and teletype-u 1000 Explained earlier to run with ubuntu user's permissions-v /home/ubuntu/data:/home/ubuntu/data to mount the directory containing the MiSeq library-v /home/ubuntu/accessoryfiles:/accessoryfiles to mount the directory created by the accessoryfiles scriptdocker-assembly is the name of our image we built earlier/home/ubuntu/data is the folder containing the MiSeq library, this parameter is passed directly to the blackbox-pipeline/home/ubuntu/data parameter in this example. The options available are found in blackbox-pipelineSampleSheet.csv is needed for the pipeline to run
These are the instructions to build a docker image containing the blackbox-pipeline.
We packaged accessoryfiles script to create a folder called accessoryfiles in the directory it was run.
At first you need to install docker. Please follow the very good instructions from the Docker project.
After the successful installation, all what you need to do is:
Build the image:
er build -t docker-assembly https://github.com/AAFC-MBB/docker-assembly.git
You may need to download the required packages for the pipeline to run, you will have to specify their location on execution
-fsSL https://raw.githubusercontent.com/AAFC-MBB/docker-assembly/master/accessoryfiles.sh | bash
er run -u $(id -u) -v path/to/fastq/data -v path/to/accessory/files:/accessoryfiles ....
For docker setup using docker-machine with openstack and the ubuntu coud image, the default user is ubuntu with uid = 1000. This will alter thhe above docker run command to the following
er run -u 1000 ...
To use a MiSeq library (fastq files including SampleSheet.csv`GenerateFASTQRunStatistics.xmlRunInfo.xml) stored inside folder labeleddatain the home folder (/home/ubuntu/`) of an OpenStack instance:
First you must download and execute the accessoryfiles script:
To download the requirements to an accessoryfiles folder
-fsSL https://raw.githubusercontent.com/AAFC-MBB/docker-assembly/master/accessoryfiles.sh | bash
docker-machine the command becomeser-machine ssh <machine name> "curl -fsSL https://raw.githubusercontent.com/AAFC-MBB/docker-assembly/master/accessoryfiles.sh | bash"
Where <machine name> is replaced with the name you used to with the docker-machine create command
er run -it -u 1000 -v /home/ubuntu/data:/home/ubuntu/data \
home/ubuntu/accessoryfiles:/accessoryfiles docker-assembly /home/ubuntu/data
The above command can be broken down into:
docker run the command line instruction run a built container-it flag for both interactive and teletype-u 1000 Explained earlier to run with ubuntu user's permissions-v /home/ubuntu/data:/home/ubuntu/data to mount the directory containing the MiSeq library-v /home/ubuntu/accessoryfiles:/accessoryfiles to mount the directory created by the accessoryfiles scriptdocker-assembly is the name of our image we built earlier/home/ubuntu/data is the folder containing the MiSeq library, this parameter is passed directly to the blackbox-pipeline/home/ubuntu/data parameter in this example. The options available are found in blackbox-pipelineSampleSheet.csv is needed for the pipeline to run