SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
https://nf-co.re/sarek
MIT License
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Unify bianca and milou configuration #215

Closed marcelm closed 7 years ago

marcelm commented 7 years ago

This is the current diff between configuration/milou.config and configuration/bianca.config:

--- bianca.config       2017-03-20 16:18:49.656447658 +0100
+++ milou.config        2017-03-20 16:18:49.721844364 +0100
@@ -117,7 +117,7 @@
     memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $RunAscat {
-    module = ['R/3.3.2']
+    module = ['R/3.2.3']
     cpus = 1
     memory = {params.singleCPUMem * 2 * task.attempt}
   }

Is this worth keeping two separate files?

szilvajuhos commented 7 years ago

No, but there is no 3.3.2 on bianca yet. In fact it is not working on bianca in general, so we can update to 3.3.2, ask UPPMAX to fix R packages and use a single common UPPMAX config file.

marcelm commented 7 years ago

Has anyone been in contact with Uppmax support, yet?

szilvajuhos commented 7 years ago

Yes, but there were so many mails back and forth that it was lost in details. I can give an other shot again.

szilvajuhos commented 7 years ago

Looks R 3.3.2 and R_packages 3.3.2 are available by now on both bianca and irma, so we can use a single UPPMAX settings.

marcelm commented 7 years ago

Great! I’ll send a PR.