RepeatMasker: consider offline systems / fail faster

[ptrebert]

Hi,

a suggestion for improving usability when setting up RepeatMasker in a conda environment: consider adding parameters such as --timeout=30 --tries=3 to the wget call and handle wget's exit code 4 (Network failure) explicitly. For example, print an info message informing the user that the on-the-fly lib download failed (line 14) and that the steps listed in the post-link.sh script (line 15) need to be manually executed after getting the lib file in some other way onto the system.

https://github.com/bioconda/bioconda-recipes/blob/3d57cd399513963b25a35b5e414f0682ba6fceae/recipes/repeatmasker/post-link.sh

Use case for this are offline systems such as HPCs in clinical contexts where IT is at least providing a mirror of common conda channels but no general access to online resources.

Best,
Peter

[martin-g]

@ptrebert Do you want to send a Pull Request with the proposed changes?

[ptrebert]

if they sound reasonable, I can do that...