...
I'm pretty sure that [greg] still helps out with this, you would probably need to ask him for access. Also, if you are working off campus, you need to log into your on-campus athena account first then ssh onto coyote. If you have questions about this, just ask me. Also, put yourself on the mailing list by checking out the other link above.
What is available:
You can find out with "module avail"
modules of interest (to me):
...
(matlab above one above is 2009)
module add matlab/2012b
QIIME has been installed (both of the following commands in order!):
module add python/2.7.6
module add qiime/1.8.0
...
Also, there are different timed queues, so make sure if you get this working that it submits to the right queue. From what I can tell there is short, long and ultra. Not sure what the exact compute times are for eachIf you type qstat -q you can see a list of queues and how many running and queued items each has. At the time I checked there are six queues: speedy, short, long, quick, be320, and ultra. These have different allowed runtimes.
From Mark and Chris-
I've been using a script chris wrote which works pretty well:/home/csmillie/bin/ssub
What it does
It streamlines job submission. If you give it a list of commands, it will (1) create scripts for them, and (2) submit them as a job array. You can give it the list of commands as command line arguments or through a pipe.
Quick examples
1. Submit a single command to the cluster ssub "python /path/to/script.py > /path/to/output.txt"
2. Submit multiple commands to the cluster (use semicolon separator) ssub "python /path/to/script1.py; python /path/to/script2.py"
3. Submit a list of commands to the cluster (newline separator) cat /list/of/commands.txt | ssub
Detailed example /home/csmillie/alm/mammals/aln/95/
In this directory, I have 12,352 fasta files I want to align. I can do this on 100 nodes quite easily:
1. First, I create a list of commands: for x in `ls *fst`; do y=${x%.*}; echo muscle -in $x -out $y.aln; done > commands.txt
...
pick_rep_set.py -i ${DATA}fwd_otu/uclust_picked_otus${PBS_ARRAYID}/ML1-${PBS_ARRAYID}_filt_otus.txt -f ${DATA}fwd_filt/dropletBC/ML1-${PBS_ARRAYID}_filt.fna -o ${DATA}fwd_otu/repSet/ML1-${PBS_ARRAYID}_rep.fna
Installing and Running Slime on coyote (also note the trick about installing packages below):
ssh onto super-genius
Clone slime into the ~/lib/:
git clone https://github.com/cssmillie/slime.git
Then add r/3.0.2
module add r/3.0.2
I wanted to install some package in R, but I couldn't get them directly, so I did the following:
In R:
> Sys.setenv(http_proxy="http://10.0.2.1:3128")
Then it should work.
install.packages('optparse')
install.packages('randomForest')
install.packages('ggplot2')
install.packages('plyr')
install.packages('reshape')
install.packages('car')
(However, I'm still having trouble running slime)
If i exit out now try to run these on the command line, I had some success with this (although Chris said I need to be in the slime folder because I edited run.r to include the path to until.r to work):
Rscript ~/lib/slime/run.r -m setup -x unique.f5.final.mat.transpose2 -y enigma.meta -o output > commands.sh