Closes #1680
This PR adds some small code changes that were needed to run on AWS, which indeed successfully ran! Two main code changes:
analyses/transcriptomic-dimension-reduction/04-explore-sequencing-center-effects.Rmd and associated notebook: Change in file system case sensitivity (Linux is case sensitive but Mac is not!)
For the analyses/snv-callers/run* files, I had to add some flags to ensure files indeed get overwritten - specifically, the SQL dbs and a tarball. The code fails if these files already exist, so we need overwrite flags. For this, I ended up adding some variables for this such that these overwrite flags are only used when we run for the manuscript from here: scripts/run-manuscript-analyses.sh, rather than always overwriting the sql db and tarball.
Closes #1680 This PR adds some small code changes that were needed to run on AWS, which indeed successfully ran! Two main code changes:
analyses/transcriptomic-dimension-reduction/04-explore-sequencing-center-effects.Rmdand associated notebook: Change in file system case sensitivity (Linux is case sensitive but Mac is not!)analyses/snv-callers/run*files, I had to add some flags to ensure files indeed get overwritten - specifically, the SQL dbs and a tarball. The code fails if these files already exist, so we need overwrite flags. For this, I ended up adding some variables for this such that these overwrite flags are only used when we run for the manuscript from here:scripts/run-manuscript-analyses.sh, rather than always overwriting the sql db and tarball.