Add singularity call to track_from_clusters rule
#6
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
In the rule `track_from_clusters`, `fslmaths` is called directly. This only works if `fslmaths` is installed on the system, otherwise it ambiguously errors out.
This commit instead calls `fslmaths` from the `fsl_cuda` container that is being used for `probtrackx2_gpu` (adding `singularity exec -e {params.container}`prior to the `fslmaths` call).
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
In the rule
track_from_clusters,fslmathsis called directly. This only works iffslmathsis installed on the system, otherwise it ambiguously errors out.This commit instead calls
fslmathsfrom thefsl_cudacontainer that is being used forprobtrackx2_gpu(addingsingularity exec -e {params.container}prior to thefslmathscall).