-
Notifications
You must be signed in to change notification settings - Fork 5
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
samtools hard-coded to a gsc-specific path #8
Comments
Ok, I have removed the hardcoded paths from both scripts (RAILS v1.4.1 and cobbler v0.5) and added clarity to error message. We have been using samtools v1.8 on our end. Let me know how it goes. |
Rene, |
This is a successor of SSAKE and of LINKS scaffolders. Remove hardcoded PATHs, see bcgsc/RAILS#8 (comment) Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
The hardcoded |
done. |
Both cobbler.pl & RAILS define SAMPATH to be "/gsc/btl/linuxbrew/bin/samtools"
The readme doesn't mention that it needs to be changed or that RAILS depends on samtools (any particular version?)
Without a valid samtools, the tests fail with:
Empty arrayn -- maybe the scaffold merging step did not necessitate
gap filling. at /group/bioinfo/apps/apps/RAILS_v1.4/RAILS line 215.
RAILS process terminated.
Consider checking that a valid samtools is present and print clear error message if its missing.
This bug was opened and then closed as fixed, but nothing seems to have changed.
I was using version 1.4
The text was updated successfully, but these errors were encountered: