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Last pushed: 2 years ago
Short Description
Vagrant-compatible image to run a SPAdes pipeline on fastq data in a mounted volume.
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#README

Vagrant-compatible image to run a SPAdes pipeline on fastq data in a mounted volume.

docker pull olcbio/vagrantspades

The container will require a mounted volume from the host machine containing or to contain the data sets to be run.
This can have any name on the host machine, but within the container must be named
/mnt/zvolume1/WGS_Spades until further notice.

mkdir /path/to/datavolume

You can put data folders in this volume at your leisure, both beforehand and while the container has it mounted. Each data folder inside the volume should contain fastq files and the three files:
SampleSheet.csv
RunInfo.xml
GenerateFASTQRunStatistics.xml
See the spades pipeline README available at https://github.com/adamkoziol/SPAdesPipeline/blob/master/README.md
for details.

To create the container with the volume mounted, use the -v flag:

docker run -it -v /path/to/datavolume:/mnt/zvolume1/WGS_Spades olcbio/vagrantspades

Which will put you in a bash shell within the container. From the container shell, to run a data folder through the pipeline:

SPAdesPipeline.py -p /mnt/zvolume1/WGS_Spades/datafolder

Docker Pull Command
Owner
olcbio

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