Difference: SoftwareInstallation (13 vs. 14)

Revision 142019-04-04 - ReneJanssen

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SoftwareInstallation

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  If you later just wish to install packages, you can use the cpan -i command from the command line. No need to startup the CPAN shell.
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Making software available using guix

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Making software available using GUIX

 Guix is a package manager and is installed for general use.
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Making software available using LMOD

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 #Making software available using LMOD.
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Making software available using SINGULARITY

Singularity (docker compatible but more secure) is available on the compute-nodes (n00XX).
You can download docker- or singularity- images and run your programs in singularty.
p.e. R and SAIGE module :

You can execute this in a qlogin session.

SAIGE on singularity(image)
# Download a singularty image for SAIGE:
singularity pull shub://singularity-hub.org/statgen/singularity-saige

# Login into the container
singularity shell ./statgen-singularity-saige-master-latest.simg

# Check if SAIGE is available

R
installed.packages() 
q()
n

# run a R script in the container
# create 1.R
library("SAIGE") 
print("Hello World!") 

# You can run this in a qsub script
# Run your code by :
singularity exec ./saige-0.35.8.1.simg Rscript 1.R

SAIGE on singularity with docker image

singularity pull docker://wzhou88/saige:0.35.8.1
singularity shell ./saige:0.35.8.1
R
installed.packages()
q()
n

# run
singularity exec ./saige-0.35.8.1.simg Rscript 1.R

 
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