defuse reference docs - multiple issues

[keiranmraine]

• template for defuse-config.txt should have the container paths pre-populated
  • one of the instances of ensembl version isn't expanded
• create_reference_dataset.pl is defuse_create_ref.pl
  • usage doesn't match
• can't be run in the container as wget not installed.

[alongalor]

any update on these issues?

[byb121]

any update on these issues?

Which of the three bullet points is/are bothering you as well? We probably will have to leave the second bullet point to developers of Defuse. The other two should be relatively quick to fix.

[alongalor]

Hi @byb121, thanks for the quick response! The first bullet point is of relevance to me.

Thanks for your help,

Alon

[byb121]

Hi @alongalor, After a look at the code, I believe "container path" relevant attributes: like source_directory and bin paths in defuse-config.txt will be corrected at run-time. I wonder if you've encountered an error to suggest you otherwise.