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

Allow setting config file or data-folder by parameter #244

Open
FelixMoelder opened this issue Jan 11, 2022 · 1 comment
Open

Allow setting config file or data-folder by parameter #244

FelixMoelder opened this issue Jan 11, 2022 · 1 comment

Comments

@FelixMoelder
Copy link

When installing interproscan via conda it is currently necessary to separately download the databases and add them to the interproscan folder (see post-link.sh).
While this is generally working many users will probably not noticing that this is required.
In addition there are cases where this procedure is not even applicable.
Especially when including the conda-package in a snakemake workflow.
As snakemake is maintaining conda-environments on its own it is not possible to include the database files in the environment.
This could be easily solved in two ways by allowing to:

  • define a custom interproscan.properties-file via a command line parameter
  • set the only the path of the data directory by a parameter
@abretaud
Copy link
Contributor

👍 that would be quite useful
Currently in the Galaxy tool we use this ugly trick = create a .interproscan-5/interproscan.properties file in a job specific HOME dir.

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

No branches or pull requests

2 participants