Collin Tokheim ctokheim

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.

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.

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

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.

	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

	#########################################
	# 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

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


	# 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

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