Last updated: 2017-10-24

Code version: 13f7b6a

This file describes how I will set up a conda environment to ensure the code is reproducible.

1. Start interactive session on midway2

#log into midway2
ssh brimittleman@midway2.rcc.uchicago.edu

#on midway2 start an interactive session
sinteractive  --partition=broadwl

2. Create a conda computing environment

This environment was adapted from sebastianp79/dropseq_pipeline.

module load Anaconda3

conda env create --file /project2/gilad/briana/net_seq_pipeline/environment.yaml

To update the environment, you can run the following command:

conda env update --file /project2/gilad/briana/net_seq_pipeline/environment.yaml

Session information

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.4.2  backports_1.1.1 magrittr_1.5    rprojroot_1.2  
 [5] tools_3.4.2     htmltools_0.3.6 yaml_2.1.14     Rcpp_0.12.13   
 [9] stringi_1.1.5   rmarkdown_1.6   knitr_1.17      git2r_0.19.0   
[13] stringr_1.2.0   digest_0.6.12   evaluate_0.10.1

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