Difference between revisions of "2014 Prerequisites"

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We would like all users at the BioXFEL workshop to be using the same set of ''cctbx.xfel'' sources.  To this end, please be sure you do not source any locally downloaded or installed ''phenix'' or ''cctbx'' versions in your .bashrc or .cshrc files.  Instead, follow the instructions below to use the sources installed for general users at SLAC.
 
We would like all users at the BioXFEL workshop to be using the same set of ''cctbx.xfel'' sources.  To this end, please be sure you do not source any locally downloaded or installed ''phenix'' or ''cctbx'' versions in your .bashrc or .cshrc files.  Instead, follow the instructions below to use the sources installed for general users at SLAC.
 +
 +
The below directions are for bash.  You can find the csh associated equivalents by following the linked pages.
  
 
You may find the general [[overview]] to be useful first.
 
You may find the general [[overview]] to be useful first.
Line 5: Line 7:
 
==== Set up PSDM ====
 
==== Set up PSDM ====
  
The Photon Science Data Management (PSDM) system provides pyana, and is required for reading the raw data saved by the CSPAD detector.  Follow the instructions at [[Set up PSDM software]], using the PSDM suite installed at SLAC.
+
The Photon Science Data Management (PSDM) system provides pyana, and is required for reading the raw data saved by the CSPAD detector.  Follow the instructions at [[Set up PSDM software]], using the PSDM suite installed at SLAC, or simply add this to your .bashrc file:
 +
 
 +
test -r /reg/g/psdm/etc/ana_env.sh && . /reg/g/psdm/etc/ana_env.sh
 +
 
 +
Then execute these commands from your home folder:
 +
newrel ana-current myrelease
 +
cd myrelease
 +
sit_setup
 +
newpkg my_ana_pkg
 +
 
 +
This creates a new working directory from which to execute pyana commands named myrelease, then configures it.
  
 
==== Set up ''cctbx.xfel'' ====
 
==== Set up ''cctbx.xfel'' ====
  
''cctbx.xfel'' is installed for general users at SLAC and maintained by the ''cctbx.xfel'' team.  Follow the [[Setup | setup instructions for "cctbx.xfel"]], using the SLAC sources as described.
+
''cctbx.xfel'' is installed for general users at SLAC and maintained by the ''cctbx.xfel'' team.  Follow the [[Setup | setup instructions for ''cctbx.xfel'']], using the SLAC sources as described, or simply add this to your .bashrc file:
 +
 
 +
test -r /reg/g/cctbx/build/setpaths.sh && \
 +
  . /reg/g/cctbx/build/setpaths.sh
 +
 
 +
Then, from your myrelease directory, link PSDM to cctbx.xfel as follows:
 +
cd my_ana_pkg
 +
ln -fns /reg/g/cctbx/sources/cctbx_project/xfel/cxi/cspad_ana src
 +
cd ..
 +
scons

Revision as of 14:57, 22 August 2014

We would like all users at the BioXFEL workshop to be using the same set of cctbx.xfel sources. To this end, please be sure you do not source any locally downloaded or installed phenix or cctbx versions in your .bashrc or .cshrc files. Instead, follow the instructions below to use the sources installed for general users at SLAC.

The below directions are for bash. You can find the csh associated equivalents by following the linked pages.

You may find the general overview to be useful first.

Set up PSDM

The Photon Science Data Management (PSDM) system provides pyana, and is required for reading the raw data saved by the CSPAD detector. Follow the instructions at Set up PSDM software, using the PSDM suite installed at SLAC, or simply add this to your .bashrc file:

test -r /reg/g/psdm/etc/ana_env.sh && . /reg/g/psdm/etc/ana_env.sh

Then execute these commands from your home folder:

newrel ana-current myrelease
cd myrelease
sit_setup
newpkg my_ana_pkg

This creates a new working directory from which to execute pyana commands named myrelease, then configures it.

Set up cctbx.xfel

cctbx.xfel is installed for general users at SLAC and maintained by the cctbx.xfel team. Follow the setup instructions for cctbx.xfel, using the SLAC sources as described, or simply add this to your .bashrc file:

test -r /reg/g/cctbx/build/setpaths.sh && \
 . /reg/g/cctbx/build/setpaths.sh

Then, from your myrelease directory, link PSDM to cctbx.xfel as follows:

cd my_ana_pkg
ln -fns /reg/g/cctbx/sources/cctbx_project/xfel/cxi/cspad_ana src
cd ..
scons