Running slicer scripts on headless server
You'll need:
Access to the server
Ask andrej.studen@ijs.si to setup access. You'll get a username and a password, which should be distinct from your key password and labkey access password. You log in to your account using ssh:
ssh username@merlin.fmf.uni-lj.si
Merlin is a headless server meaning that X11 based graphical interfaces are not available. All management is done through terminal based instructions. Get acquianted with BASH to help you along. As an editor I find VI/VIM priceless, but it does take a while to get used to it. To edit a file, start VIM with:
Software
Download software from git. To simplfy path setting, partially done in code, you should place your code in ~/software/src directory, and rename data-pre-processing to DORA:
cd
mkdir -p software/src
cd software/src
git clone git@wiscigt.powertheword.com:andrej.studen/SlicerLabkeyExtension.git
git clone git@wiscigt.powertheword.com:dora/data-pre-processing.git
mv data-pre-processing DORA
Access to LabKey
Since you'll perform silent login to the LabKey site, your credentials must be available to the code. Do that by placing a setup file in your ~/.labkey directory (creating it if neccesary) and adjusting the variables. The file will contain your personal data (passwords for certificate and LabKey), so protect it by allowing read-only user access once finished:
chmod a-w ~/.labkey/networkConfig.json
chmod a-r ~/.labkey/networkConfig.json
chmod u+r ~/.labkey/networkConfig.json
cd ~/.labkey
ln -s networkConfig.json Remote.json
You'll also need a separate key/certificate file. To get those from p12, do:
openssl pkcs12 -in astuden.p12 -nocerts -out astuden.key
openssl pkcs12 -in astuden.p12 -clcerts -nokeys -out astuden.crt
You should also download the CA certificate.
Setup and test the software
You should set the settings in ~/software/src/SlicerLabkeyExtension/slicerScripts/env.sh. There is a template. Since you'll be running identical binary, the only change is to set DISPLAYID, which should be unique by user. Consult andrej.studen@ijs.si to get a good number. To set the number:
cd ~/software/src/SlicerLabkeyExtension/slicerScripts
cp env.sh.sample env.sh
vi env.sh
#edit DISPLAYID to the selected value
The standard way to run a script is:
~/software/src/SlicerLabkeyExtension/slicerScripts/runSlicer.sh ~/software/src/DORA/slicerScripts/test.py
The command exits, as Slicer runs in background xpra virtual server, mimicking
graphic functionality. The output of the code is logged to ~/logs/runSlicer.log, so direct output can be tracked by:
tail -f ~/logs/runSlicer.log
Once you see a Done output, the script is done.
Running analysis scripts
The standard way to run a script is:
~/software/src/SlicerLabkeyExtension/slicerScripts/runSlicer.sh ~/software/src/DORA/slicerScripts/libraDensity.py
tail -f ~/logs/runSlicer.log
Matlab script
By default, a matlab script runLibra.m is run. Variables LIBRA, INPUTFILE and OUTDIR are set by commands prior to runLibra execution start. If you need to run other command, you can update runLibra.m script in ~/software/src/DORA/matlab directory.