Introduction- Scott's script to consolidate all of the OTU calling scripts and submit them to the cluster with one command
(smile_train: Get's you where you want to go and your happy)
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You should install in lib (bin get crowded)- each person should install their own.
Get the git from:
https://github.com/swo/smile_train
Make a lib directory unless this already exists:
mkdir lib
Lone this into the lib folder you just make using gitby using git commands:
git clone https://github.com/swo/smile_train
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(open the html file within the _build folder on the Desktop to get really good documentation)
Alter the configAlter train.file cfg (you either have to link to usearch etc) to have your new names for the following (for example I changed these):
[User]
username=spacocha
tmp_directory=/net/radiodurans/alm/spacocha/tmp
library=/net/radiodurans/alm/spacocha/lib/smile_train
bashrc=/net/radiodurans/alm/spacocha/lib/smile_train/bashrcs/coyote.sh
Then, make the tmp_directory:
mkdir /net/radiodurans/alm/spacocha/tmp
You can have a detailed description of anything by using --help.
This will source the bashrc that script that Scott made.
Submit from the head node (when you log on), and if it's long, you;re going to have to use this:
ssh coyote
screen
Now you are inside screen (screen -ls will tell you which ones you are running):
You can name the screens
screen -S SPtest
and screen reattach will give you
screen -R SPtest
you can detatch and keep running:
RUN COMMAND
contol^A D
(or type man screen to get information)