Leginon

h1. 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  "Leginon Bulletin Board":http://emg.nysbc.org/bb/viewforum.php?f=2  searching

for "install" if you run into problems.

h2. 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|

h2. 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.

h2. Check out SVN Source Files from the depository

From a text

terminal:<pre>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</pre>

h2. 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

<pre>cd Leginon

python syscheck.py</pre>

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.

h2. 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

<pre>cd /usr/lib/python/site-packages

rm -r Leginon</pre>

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

h2. 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

<pre>cd leginon

python setup.py install</pre>

h2. 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:<pre>python> import sinedon

python> sinedon</pre>

*  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.

<pre>[robot2]

db: dbemdata</pre>

h2. Transfer Drift adjustment preference to use Transform Manager

* This procedure copies all most recent user settings to that required by the new

transform

manager.<pre>cd leginon

python update16.py</pre>

*  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.

<pre>[robot2]

db: dbemdata

</pre>

h2. 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.

h2. Install updated dbemtools

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

Installation Chapter.

h2. Reset installation status in projectdb

You can do this directly by mysql commands.

> mysql

projectdata<pre>> mysql projectdata -u usr_object

mysql> drop table install;

mysql> exit</pre>

Alternatively, you can use phpMyAdmin to achieve this by visiting the database, find the

table and click on drop.

h2. Install updated tools for project management

See <link linkend="install_projecttools">projecttools installation</link> section in

Complete Installation Chapter.

h2. 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.