Makefile for generating data, cluster scripts, batching create_gene_summary #5
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
However, depmap_tables expects gene_summary in RData (not feather) format make: *** No rule to make target `data/gene_summary.RData', needed by `data/master_top_table.Rdata'. Stop.
|
@hirscheylab I've run the Makefile on HARDAC and uploaded the data to DDS. I'll next be loading the data onto the web server and sharing the files with you. The Makefile should work on your machine as well as the cluster, but let me know if you have questions. |
This was referenced Dec 12, 2019
johnbradley
added a commit
to Duke-GCB/ddh
that referenced
this pull request
Jan 21, 2021
…r-105 Merge ddh PR matthewhirschey#105
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Outdated suggestions cannot be applied.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.
create_gene_summary.Rto fetch gene summaries in batches (significant speedup) and save output as Rdata (instead of feather)build-slurm.shandupload-slurm.shscripts for generating data on HPC cluster and uploading results to data service.