...
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
...
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 packages in R (for Slime but it might work in other ways):
ssh onto super-genius
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)