Difference between revisions of "Install DOCK 3.7"

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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 02:14, 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.