avoid repeating to build SIF image for Singularity: use local SIF image if an env variable LOCAL_SIF_PATH is set

[szcf-weiya]

When I run the program in the cluster with Singularity, I found that it takes a long time to build a SIF image. And for another run, it again takes a long time to build image, it seems that the cached image in .singularity folder does not help. Here is the running time (330s)

> library(dyno)     
> x = matrix(rpois(9900, 1), nrow = 99)                                                                                                                                               
>     rownames(x) = 1:nrow(x)                                                                                                                                                         
>     colnames(x) = 1:ncol(x)                                                                                                                                                         
>     dataset = wrap_expression(counts = x, expression = log(x+1))     
> system.time({infer_trajectory(dataset, "comp1", debug=T)})                                                                                                                          
Running singularity exec 'docker://dynverse/ti_comp1:v0.9.9.01' echo hi
Running /usr/bin/singularity exec --containall -B \ 
  '/tmp/RtmpzcjE6q/file32c7f55a74b8e9/:/copy_mount,/tmp/RtmpzcjE6q/file32c7f541ac7236/tmp:/tmp2' \ 
  'docker://dynverse/ti_comp1:v0.9.9.01' cp /code/definition.yml /copy_mount/
Executing 'comp1' on '20231227_181629__data_wrapper__jSj89c7coa'        
With parameters: list(dimred = "pca", ndim = 2L, component = 1L) 
...
...
                                                                                                              
Running /usr/bin/singularity exec --containall --pwd /ti/workspace -B \
  '/tmp/RtmpzcjE6q/file32c7f542b877db/ti:/ti,/tmp/RtmpzcjE6q/file32c7f54c14b061/tmp:/tmp2' \
  'docker://dynverse/ti_comp1:v0.9.9.01' bash
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:bd5da474b8baade003eb744e862574f758b269c20cd2bc0d3c6860e1b3b4e08a
Copying blob sha256:844c33c7e6ea19e3f6847e0667befdfb3ef02d6fc735b22c2d070261b6263b97
...
...

INFO:    Using cached SIF image      
   user  system elapsed 
309.030  12.012 330.661 

To avoid repeating to build the SIF image, I introduce an environment variable, LOCAL_SIF_PATH. If the variable is set, then pull the image and save as .sif locally via

singularity pull xxxx.sif docker://

To align with the existing code, if the env variable is unset, then just run as before.

After saving to a local SIF image, we can speed it up significantly --- only around 2 seconds for the same dataset.

devtools::install_github("szcf-weiya/babelwhale")
Sys.setenv(LOCAL_SIF_PATH=getwd())

user  system elapsed
  0.865   0.663   1.952