Last updated: 2020-09-23

Checks: 2 0

Knit directory: misc/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: d2b54b1

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The results in this page were generated with repository version d2b54b1. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/deconvSimulation2.Rmd
    Untracked:  analysis/ideas.Rmd
    Untracked:  code/sccytokines.R
    Untracked:  code/scdeCalibration.R
    Untracked:  data/bart/
    Untracked:  data/cytokine/DE_controls_output_filter10.RData
    Untracked:  data/cytokine/DE_controls_output_filter10_addlimma.RData
    Untracked:  data/cytokine/README
    Untracked:  data/cytokine/test.RData
    Untracked:  data/cytokine_normalized.RData
    Untracked:  data/deconv/
    Untracked:  data/scde/

Unstaged changes:
    Modified:   analysis/deconvSimulation.Rmd
    Modified:   analysis/deconvolution.Rmd
    Deleted:    data/mout_high.RData
    Deleted:    data/scCDT.RData
    Deleted:    data/sva_sva_high.RData

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/command.Rmd) and HTML (docs/command.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd d2b54b1 DongyueXie 2020-09-23 wflow_publish(c(“analysis/index.Rmd”, “analysis/genelength.Rmd”,
html 53029fc Dongyue Xie 2020-01-15 Build site.
Rmd cfac861 Dongyue Xie 2020-01-15 wflow_publish(“analysis/command.Rmd”)
html 1313b6f Dongyue Xie 2019-12-12 Build site.
Rmd c07c0dc Dongyue Xie 2019-12-12 wflow_publish(“analysis/command.Rmd”)

Introduction

cd $SCRATCH

htop: check login mode cpu use

Get compute node:

sinteractive --time=10:00:00 --mem=8G -c 4 -p mstephens --account=pi-mstephens

--exclusive:

squeue -u dyxie : see job status

squeue -p mstephens: see who’s using nodes.

scontrol show node=midway2-0437

squeue -p broadwl | less -S

export OPENLABS_NUM_THREADS=4: use 4 cpus to compute

Open another command window, login to midway2 then ssh midway2-0437, htop --user=dyxie monitor the computations on the other command window.

Use screen to back up screens.

nano myscript.R to write an R script.

module load R then Rscript myscript.R

sbatch myscript.sbatch

parallel in linux command

Unzip (Open) Gz File

gzip -d file.gz or gunzip file.gz

Preview files

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