How to Update from v15 (Linux)¶

The changes from v1.5 requires update of all in-house components of Leginon and dbemtools,
but not the database nor mrctools. instruments.cfg should be modified on each microscope host.
Don't forget that you need to also update the packages on the microscope-controlling computer
since the pyScope update need to be synchronized.

See <link linkend="InstT_install">Installation Troubleshooting</link> and the Leginon Forum searching
for "install" if you run into problems.

Packages required from NRAMM¶

Here are the packages you need to install with python installer

SVN Package Name	Installed Python Package Name	Reason for update:
numextension	numextension	none
libcv	libCV	bug fixes
leginon	Leginon	new features
pyami	pyami	clean up
sinedon	sinedon	new stuff
pyScope	pyScope	new instrument configuration
ImageViewer	ImageViewer	updated and required for tomography

Download and install SVN client program:¶

By switching to svn package check out, you now need to install svn client. The rpm
package probably has the word "svn" or "subversion" in its name.

Check out SVN Source Files from the depository¶

From a text
terminal:

mkdir Leginon-1.6-ALL
cd Leginon-1.6-ALL
svn co http://emg.nysbc.org/svn/leginon/branches/1.6 Leginon
svn co http://emg.nysbc.org/svn/pyami/branches/leg1.6 pyami
svn co http://emg.nysbc.org/svn/pyScope/branches/leg1.6 pyScope
svn co http://emg.nysbc.org/svn/sinedon/branches/leg1.6 sinedon
svn co http://emg.nysbc.org/svn/numextension/branches/leg1.6 numextension
svn co http://emg.nysbc.org/svn/libcv/branches/leg1.6 libcv
svn co http://emg.nysbc.org/svn/ImageViewer/branches/leg1.6 ImageViewer

Perform system check:¶

In addition to the downloads from our svn depository, there are several other
requirements that you will get either from your OS installation source, or from its
respective website. The system check in the Leginon package checks your system to see if you
already have these requirements

cd Leginon
python syscheck.py

You should have all the supporting packages installed for v1.5. If you see any lines
like "*** Failed...", then you have something missing. Otherwise, everything should result
in "OK". Note that numpy and scipy are now required by the new version even if you don't run
tomography. numarray is no longer used.

Uninstall your existing packages:¶

At the beginning of the syscheck.py output, the location of the exisiting Leginon folder
is shown. Although new installation overwrite the old in most cases, problem has been
observed in the past. Therefore, it is best to remove the old files before new
installation.

For example, your Leginon folder is at /usr/lib/python/site-packages/Leginon

cd /usr/lib/python/site-packages
rm -r Leginon

Be aware that in some cases the installed package name is different (capitalized) from
your svn package name and that numextension amd libCV are not in its own subdirectory in the
python library but just the compiled .so files

Install the packages you downloaded from NRAMM svn depository¶

• run syscheck.py again to make sure you have everything.

• Reinstall the package in each folder with commands such as
  

  cd leginon
  python setup.py install

Modify sinedon.cfg if you use grid-inserting robot¶

• Find your sinedon.cfg. Depending on your previous setting, look in the
  directories listed here in order:
  *your home directory as described in syscheck.py
  *The sinedon directory where it is called from. If unsure, start python command
  line and type these to find
  out:

  python> import sinedon
  python> sinedon

• Add the following database configuration. The Robot2 module uses the database to
  communicate to the robot. Applications that carries the name "Robot" requires this to be
  set. In general, using the same database as the general leginon database is fine.

[robot2]
db: dbemdata

Transfer Drift adjustment preference to use Transform Manager¶

• This procedure copies all most recent user settings to that required by the new
  transform
  manager.

  cd leginon
  python update16.py

• Add database configuration if you intend to use grid-inserting robot. The Robot2
  module uses the database to communicate to the robot. Applications that carries the name
  "Robot" requires this to be set. In general, using the same database as the general
  leginon database is fine.

[robot2]
db: dbemdata

Install updated mrc module¶

php-mrc 1.5 uses fftw3. You may need to install that before installing the tool as a php
extension.

See <link linkend="install_mrc">php-mrc extenstion installation</link> section in
Complete Installation Chapter.

Install updated dbemtools¶

See <link linkend="install_dbemtool">dbemtools installation</link> section in Complete
Installation Chapter.

Reset installation status in projectdb¶

You can do this directly by mysql commands.

mysql

projectdata

> mysql projectdata -u usr_object
mysql> drop table install;
mysql> exit

Alternatively, you can use phpMyAdmin to achieve this by visiting the database, find the
table and click on drop.

Install updated tools for project management¶

See <link linkend="install_projecttools">projecttools installation</link> section in
Complete Installation Chapter.

Load default node settings for Leginon applications (optional)¶

Default settings are useful for new users of a new application. However, if you have
manually set these as administrator user in Leginon, loading these now will "overwrite" your
settings.

See <link linkend="admin_load_defaults">admintools default loading</link> section in
Complete Installation Chapter.