bigSCale is a complete framework for the analysis and visualization of single cell data. It allows to cluster, phenotype, perform pseudotime analysis, infer gene regulatory networks and reduce large datasets in smaller datasets with higher quality.
Allocate an interactive session and run the program. Sample session:
[user@biowulf ~]$ sinteractive --mem=4g salloc.exe: Pending job allocation 49998864 salloc.exe: job 49998864 queued and waiting for resources salloc.exe: job 49998864 has been allocated resources salloc.exe: Granted job allocation 49998864 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn0868 are ready for job srun: error: x11: no local DISPLAY defined, skipping [user@cn0868 ~]$ module load bigSCale2 [+] Loading singularity 3.5.3 on cn0868 [+] Loading bigSCale2 20191119 ... [user@cn0868 ~]$ bigSCale2 INFO: You are now opening a new shell within a Singularity container. Your INFO: environment will change and you will have access to a different set of INFO: commands and executables. Please remember to exit this shell when you are INFO: finished with your session. WARNING: Bind mount '/home/user => /home/user' overlaps container CWD /home/user, may not be available Singularity> R R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(bigSCale) [snip...] > quit() Save workspace image? [y/n/c]: n Singularity> exit exit [user@cn0868 ~]$ exit exit salloc.exe: Relinquishing job allocation 49998864 [user@biowulf ~]$