First of all thank you for the work you have done on this package.
I am currently facing a problem when using infer_trajectory on my HPC (SGE).
My HPC can not pull containers, the workaround I used for other projects was to pull the image localy and then to copy it on the HPC, and there was no error in this way.
Is there way to use a already pulled container, such as :
model <- infer_trajectory(dataset, "{path}/ti_slingshot_v1.0.3.sif", verbose = TRUE, parameters = list(reducedDim = as.matrix(umap), clusterLabels = label, start.clus = "Group1", end.clus = c("Group2"), times = days)
Running singularity exec \
'docker:///{path}/ti_slingshot_v1.0.3.sif' \
echo hi
Error in processx::run("singularity", c("exec", paste0("docker://", container_id), :
System command 'singularity' failed, exit status: 255, stderr:
E> FATAL: Unable to handle docker:///{path}/ti_slingshot_v1.0.3.sif uri: failed to get checksum for docker:///{path}ti_slingshot_v1.0.3.si
f: unable to parse image name docker:///{path}/ti_slingshot_v1.0.3.sif: invalid reference format: repository name must be lowercase
I can not run dynwrap::test_singularity_installation(detailed = TRUE) since pulling is not possible on HPC.
> system("singularity exec '{path}/ti_slingshot_v1.0.3.sif' echo hi")
INFO: Converting SIF file to temporary sandbox...
hi
INFO: Cleaning up image...
Hello,
First of all thank you for the work you have done on this package. I am currently facing a problem when using infer_trajectory on my HPC (SGE). My HPC can not pull containers, the workaround I used for other projects was to pull the image localy and then to copy it on the HPC, and there was no error in this way.
Is there way to use a already pulled container, such as :
I can not run
dynwrap::test_singularity_installation(detailed = TRUE)since pulling is not possible on HPC.Best, Simon Chevolleau