/saccharis-docker

Primary LanguageDockerfile

Saccharis-docker

This is a Docker container for the Saccharis pipline to characterize CAZymes.

Requirements

  • Docker
  • A local copy of the cazy_extract.pl script (commes with SACCHARIS) which contains an individual NCBI API. You can get one here.

Modifications to cazy_extract.pl

A description of what you have to do can also be found on the Saccharin Github page: https://github.com/DallasThomas/SACCHARIS

  • Sign up for an NCBI account and get a personal API key.
  • Change the lines 31-33 in your local cazy_extract.pl file according to the information from your NCBI account.
  • When you run the container, bindmount the directory containing the modified cazy_extract.pl to your containers /usr/local/external directory.

Run the saccharis container

In this example the folder where this command is executed contains a folder called bin which contains the modified cazy_extract.pl file. The tmp folder is used by prottest, to save intermediate files in case they want to be kept and sinspected manually outside the container.

$ docker run --rm -it -v $(pwd):/data -v $(pwd)/bin:/usr/local/external -v $(pwd)/tmp:/tmp reslp/saccharis:1 Saccharis.pl -d /data -g characterized  -f GH5 -t 8