Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add bclConvert in the Singularity Container #38

Open
wants to merge 4 commits into
base: bclConvert_centos7
Choose a base branch
from

Conversation

lehmann-ju
Copy link

  • add bclConvert in the singularity container
  • fix conda environment in the singularity container
  • update pip since virtualenv required a newer version + solve all dependencies
  • update the github workflow since it wont install Singularity correctly
  • get the installation file of bcl-convert via wget using a secret

It is necessary to add a secret BCL_CONVERT_INSTALLER to the bcl-convert installation file (f.e.: https://webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-4.0.3-2.el7.x86_64.rpm) and a secret SINGULARITY_TOKEN for the access token to Sylabs.io.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant