Commands that I always forget

commands.sh

# To ask for more writing memory:
-l h_fsize=40G

# Tar

tar -xvfz

# To remove all deleted files from git repo: 
git rm $(git ls-files --deleted)

# In R:
i=as.numeric(commandArgs(TRUE)[1])

# To delete all my jobs on the cluster:
qdel -u jfortin

# To create a symbolic link: 
ln -s {/path/to/file-name} {link-name}

# What to put in a shell script to run an R job with 2 parameters:
Rscript yourScript.R $1 $2

# Example of for loop in shell:
for i in {1..8}
do
	qsub -cwd -V -l mem_free=10G,h_vmem=12G yourScript.sh $i;
	sleep 50
done


# To get all the files from a directory
wget -r -np -k -nd http://www.something.com/directory/

# To name screen sessions:
screen -S yourName


# Useful R commands:
pmin, pmax, ifelse

# Useful Unix commands:
comm, join, merge, cut, jobs, "&" after running a command, fg, tee, cd -, 

# 
curl ftp://path/file.txt.gz | gunzip -cd | head

# To count how many jobs are running:
qstat | cut -d " " -f 10 | grep "r" | wc -l