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SLURM

Slurm is a job scheduler for computer clusters. This document is based on this tutorial. A useful guide showing the relationships between SGE and SLURM is available here.

Gathering information

Two commands may be useful:

• sinfo provides information about the resouces of the cluster.

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# Using -np flag just prints out what the planned execution is
snakemake -np mapped_reads/A.bam

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# create a new environment with a file specifying the required packages
# -c bioconda adds a channel for bioinformatic packages
conda create -n myenv_name -c bioconda --file requirements.txt

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Some useful colors

• niobium - turqouise-like
• smudge - pale green
• wheat - tan

Display biological unit

To display the biological unit for the PDB structure, the split_state command is used.

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library(lme4)
library(ggplot2)

#create some levels
levs <- as.factor(c("l1","l2","l3","l4","l5"))

#set the factor means
f_means <- c(6,16,2,10,13)

# set individual as a factor

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#########################################
# Convert Sam to Bam with a header:
# -b output bam
# -S input sam
#########################################
samtools view -bS sample.sam > sample.bam

#########################################
# convert Sam to Bam without a header
# -b output bam

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# remove \r from file
cat myfile.txt | perl -p -e 's/\r//g' > output.txt

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Install VIM Locally

Go to VIM website and download VIM:

$ wget ftp://ftp.vim.org/pub/vim/unix/vim-7.4.tar.bz2
$ tar xjf vim-7.4.tar.bz2
$ cd vim74
$ mkdir -p ~/local
$ ./configure --prefix=/home/username/local

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Command Line Running

The following line will run the function and then drop into the interactive matlab shell when finished.

matlab -nodisplay -nojvm -nosplash -nodesktop -r "MyFunc('param1')"

However if you don't want to drop into the matlab shell, then you need to add an exit statement to the end of the command.