Comments (1)
xihaoli
commented on September 25, 2024
Hi @pthami07,
Thanks for your interest in STAARpipeline. For the usage of docker as a singularity image file (sif), below are some example scripts for Slurm Workload Manager:
### Example 1: use sif to run an interactive R
salloc -p test -n 1 -t 00-08:00 --mem=6000 singularity shell staarpipeline_0.9.6.sif
R
### Example 2: use sif to run a single R script
salloc -p test -n 1 -t 00-08:00 --mem=6000 singularity shell staarpipeline_0.9.6.sif
R CMD BATCH Association_Analysis_PreStep.r
### Example 3: use sif in batch jobs
sbatch STAARpipeline_Gene_Centric_Coding.sh STAARpipeline_Gene_Centric_Coding.r
Note: In STAARpipeline_Gene_Centric_Coding.sh of Example 3, change /n/.../Rscript to singularity exec staarpipeline_0.9.6.sif Rscript
Best,
Xihao
from staarpipeline-tutorial.
Related Issues (20)
- fit_nullmodel Output is mostly Null and 0 HOT 16
- Fitting NULL model for binary outcomes HOT 5
- Error in Gene Centric Analysis HOT 1
- Error in results_plof_genome[, "cMAC"] : subscript out of bounds HOT 2
- Followup Question to Issue #28 HOT 2
- STAARpipeline_Gene_Centric_Noncoding HOT 2
- Dynamic Window dim(X) error HOT 3
- Can't annotate individual variant results HOT 2
- [Suggestion-Implementation] Add information to summary and annotations of results HOT 1
- Conditional analysis - Summary Gene Centric Noncoding not running to completion HOT 6
- Ukbiobank Agds files generation HOT 16
- Plots for gene centric ncRNA regions HOT 5
- FATAL ERROR - Too many first alleles as the major allele (~21.5%). HOT 1
- warning messages in generating the annotated GDS (aGDS) file. HOT 3
- Controls / cases counts inverted when using binary model HOT 7
- kinship matrix HOT 2
- variant set in gene-centric coding/noncoding analysis HOT 2
- in the Step 2: Individual (single-variant) analysis, Error in if (chr == 1) { : argument is of length zero HOT 3
- Error : Mat::operator(): index out of bounds & Error in apply(emthr_SCANG_O, 2, max) : HOT 1
- What is the difference between the "results_temp" and "results_m" results? HOT 1
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from staarpipeline-tutorial.