Install DOCK 3.7: Difference between revisions
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If you do not already have a cluster with middleware, see: [[So you want to set up a lab]]. | If you do not already have a cluster with middleware, see: [[So you want to set up a lab]]. | ||
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= Our software = | = Our software = |
Revision as of 09:14, 13 March 2014
If you do not already have a cluster with middleware, see: So you want to set up a lab.
Our software
Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html
mkdir -p ~/code/DOCK cd ~/code/DOCK tar xzf dock3.7.tgz
set up .cshrc (or .bashrc equivalent)
You need to create something like this, depending on your exact circumstances.
setenv DOCKBASE /raid4/people/mattchu/code/DOCK set path = ($path $DOCKBASE/bin) setenv AMSOLEXE $DOCKBASE/bin/amsol-mod4 setenv OE_DIR /raid3/software/openeye/current alias pymol ~/pymol/pymol if ( $?PYTHONPATH ) then if ( `echo $PYTHONPATH | grep -c 'openeye/python'` == 0 ) then setenv PYTHONPATH $OE_DIR/python:${PYTHONPATH} endif else setenv PYTHONPATH $OE_DIR/python endif
Test 1: Basic tests
This will tell you quick what you forgot to install or if there is any obvious problem with your installation. If you can pass the tests, you are ready to proceed to the following steps.
cd ~/$DOCKBASE/test ./all-test.sh
This should run about 10-30 minutes depending on your hardware, and should either produce clear error messages (work needed) or a clear message that the tests succeeded without problems.