Appion

h1. Complete Installation

h2. Four Parts of Leginon System

<graphic fileref="http://emg.nysbc.org/software/leginon/images/images/Leg_Proj_parts.png"

format="PNG"/>

Leginon as a system that we distribute can be divided into three parts:

h2. Processing Server (Python-side)

Python (and some c) scripts that handle instrument control, data acquisition, and

processing.

h2. Database Server (MySQL-side)

a MySQL server that handles the database

h2. Web Server (PHP-side)

This includes php and Java scripts at a webserver that we will create to retrieve image

and metadata from the database and file-storage system.

h2. File Server

This is up to you to set up to store lots of data coming out of Leginon system.

h2. What is in this chapter

Leginon runs under both the Linux and Microsoft Windows Operating systems. However, the

current php-mrctool can not be installed on Windows which means mrc images can not be viewed

on the web. See the section on Possible Computer Set-up Configurations for details.

The many components for the Leginon system are divided into packages and need to be

installed separately. It has been integrated with several third party software packages that

are necessary for its operation. The installation documentation will describe how to set-up

Leginon and give hints as to how to install and set-up the necessary third-party software.

This documentation is not intended to support the additional, but necessary third-party

software.

There has been interest in installing Leginon under Mac OS X. While this is possible in

theory, we have not been successful in installing a fully functional system. The two main

problems are (1) compilation of php-mrctool from the pre-installed php and (2) wxPython on Mac

is unable to hide bitmap objects which makes Leginon graphical user interface difficult to

use.

See <link linkend="InstT_install">Installation Troubleshooting</link> and "Leginon Bulletin Board":http://emg.nysbc.org/bb/viewforum.php?f=2searching

for "install" if you run into problems.

h2.  Possible Computer Set-up Configurations

Computer(s) used for the whole Leginon system need to support five functions:

*  TEM/Camera control and data output (by python-side packages of Leginon

system)

*The computer attached to the microscope/camera is used for this function.

Therefore, it is on a Windows computer.

*  General Leginon operation such as target selection and image processing (processing

server of Leginon system)

*  Image data storage.

*  Other meta-data storage through MySQL database (by database server of Leginon

system)

*  Web server (using PHP-side of Leginon system).

*Important* The MRC module that is used to load mrc formatted files to the web

pages is not compiled on Windows. Therefore, this function must be on a linux box unless

you don't need to see the images***

The five functions can be distributed to five different computers on a network or all on

one single computer. However, since the latter minimal setup requires the use of the computer

attached to the microscope for all functions, it is not advisable.

Processing server of Leginion is a multi-platform software, meaning it can run on both

Microsoft Windows and Linux. It is also inherently designed to utilize distributed systems on

a network. MySQL used in the database server is also supported by multiple platforms. This is

not true for the Web server because the custom MRC module used in the web viewer only compiles

on linux machines. Therefore, one of the computer not part of the microscope must be a linux.

The following examples show several arrangements that take advantage of distributed system.

Other combinations are possible, but will basically be variations on one of the following

themes.

h2.  A: 1 Windows computer (attached to the Microscope) & 1 Linux computer (for all

other functions, separate from the Microscope) (Good for single user and small-scale

acquisition)

*  Install the latest processing server side of Leginon release (and supporting

packages) on the Windows computer controlling the microscope and on the Linux computer

which is to run Leginon image acquisition and processing.

*  Install the additional modules needed for CCD camera and film interaction on the

Windows computer controlling the microscope.

*  Install MySQL, PHP, the Apache Web Server, and dbem tools only on the Linux

computer that will perform these functions, (i.e. NOT the computer controlling the

microscope).

h2.  B: 1 Windows computer (attached to the Microscope) & 4 Linux computers (one for

each function) (Good for multiple microsopes, users and large-scale acquisition)

This is the set-up at NRAMM. It has the processing server side of Leginon installed on

the Windows computer attached to the microscope and on the Linux computer that is used for

running Leginon. A second Linux machine is dedicated to the database while the web-based

viewer is hosted by another server.

*  Install the python-side Leginon (and supporting packages) on the Windows computer

controlling the microscope and on the Linux computer that is to run Leginon. You can

make the latter installation accessable to any numbers of linux computers on your

network.

*  Install MySQL, PHP, the Apache Web Server, and dbem tools on the second Linux

computer that will serve as the database/web server/PHP host.

*  The computer hosting the data storage should be accessable by all linux

boxes.

h2.  C: 1 Windows computer (attached to the Microscope), 1 Windows computer running python-

and MySQL-side functions and 1 Linux computer as web server (Has been applied

successfully)

The data storage may be on one of these computers that is accessable by other

computers.

h2.  Ports that Leginon system uses:

This information is useful if you want to open specific ports between computers with a

firewall in between.

* MySQL normally uses port 3306 (but configurable in /etc/my.cnf)

* Leginon Client running on TEM host: port 55555

* Leginon main program on the processing server: dynamically assigned ports between

49152 and 65535

There is no strict port assignment since we could potentially have more than one

Leginon process running on the same linux host talking to different TEM hosts. It is

probably good enough if you only worry about opening up the first few of those ports in

your firewall (maybe 49152 through 49160, or something like that).

See more discussion at Leginon bulletin board thread on ""network problem, Leginon not seeing

tecnai host":http://emg.nysbc.org/bb/viewtopic.php?t=7"

h2. Where to Register and download Leginon system

"http://www.leginon.org/":http://www.leginon.orgis the home. Please

register if you want to recieve support from Leginon team.

*  python-side Leginon packages

direct link: "http://emg.nysbc.org/software/leginon/":http://emg.nysbc.org/software/leginon/

*  mrctools: including the tools for reading mrc images on the web

direct link: "http://emg.nysbc.org/software/mrctools/":http://emg.nysbc.org/software/mrctools/

*  dbemtools: including the tools for administration and webviewing

direct link: "http://emg.nysbc.org/software/dbemtools/":http://emg.nysbc.org/software/dbemtools/

*  project tools (optional): For administration and webviewing of projects

direct link: "http://emg.nysbc.org/software/dbemtools/":http://emg.nysbc.org/software/dbemtools/

h2.  Processing server-side Leginon Installation

For the lack of better name, processing server-side Leginon refers to packages that

performs the general functions of image acquisition and processing. The instructions here are

for Linux. Refer to Windows Installation for Windows specific instructions.

h2. Download svn checkout script from Leginon website

"http://www.leginon.org/":http://www.leginon.org/Download

svnget-1.6.sh to a convenient location such as your home directory.

h2. Check out SVN Source Files from the depository

run svnget-1.6.sh. It does the

following:<programlisting>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>

If the process fails, you probably do not have svn client installed. Skip to "Install

the supporting packages first if missing:", then try this again.

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 your_download_area/Leginon-1.6-ALL/Leginon

python syscheck.py</pre>

If python is not installed, this, of course will not run. If you see any lines like "***

Failed...", then you have something missing. Otherwise, everything should result in

"OK".

h2.  Install the supporting packages first if missing:

Follow the instruction for your specific Linux distribution.

For example, SUSE users can use YaST to install them; RedHat and CentOS users can use

yum.

*SciPy may not build properly on some versions of SuSE due to an incompatible LAPACK

package that comes with SuSE. You can get scipy as well as a compatible LAPACK etc. from

http://repos.opensuse.org/science (need to specify your SuSE version and machine

etc.)

h2.  Required supporting packages:

|_.Name:|_.Download site:|_.yum package name|_.SuSE rpm name|

|Python 2.4 or newer|"http://www.python.org":http://www.python.org|python|python-devel|

|wxPython 2.5.2.8 or newer|"http://www.wxpython.org":http://www.wxpython.org|wxPython|python-wxGTK|

|MySQL Python client 1.2 or newer|"http://sourceforge.net/projects/mysql-python":http://sourceforge.net/projects/mysql-python|MySQL-python|python-mysql|

|Python Imaging Library (PIL) 1.1.4 or newer|"http://www.pythonware.com/products/pil/":http://www.pythonware.com/products/pil/|python-imaging|python-imaging|

|Python XML module 0.8.3 or newer|"http://pyxml.sourceforge.net":http://pyxml.sourceforge.net|PyXML|python-xml|

|NumPy 1.0.1 or newer|"http://www.scipy.org":http://www.scipy.org|numpy|numpy|

|SciPy 0.5.1 (tested, others may work)*|"http://www.scipy.org":http://www.scipy.org, "http://repos.opensuse.org/science":http://repos.opensuse.org/science*|scipy|python-scipy|

*SciPy may not build properly on some versions of SuSE due to an incompatible LAPACK

package that comes with SuSE. You can get scipy as well as a compatible LAPACK etc. from

http://repos.opensuse.org/science (need to specify your SuSE version and machine

etc.)

h2.  Optional supporting packages:

*  For using Matlab to explore holefinding algorithm (Matlab HoleFinder)

pymat: "http://sourceforge.net/projects/pymat":http://sourceforge.net/projects/pymat

h2. Install the packages you downloaded from svn depository

Here are the packages you need to install with python installer inside the

Leginon-1.6-ALL folder.

|_.Name:|_.Purpose:|

| Leginon|modular TEM image acquisition|

| pyami|general functions|

| pyScope|microscope control and monitoring|

| sinedon|Leginon/database interaction|

| numExtension|c extension for numerical processing|

| libCV|small c library of algorithm from computer vision field|

| ImageViewer|image viewing for tomography|

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

*  Install the package in <emphasis role="bold">each folder</emphasis> with commands

like

these<pre>cd /your_download_area/Leginon-1.6-ALL/Leginon

python setup.py install

cd ../pyami

python setup.py install

cd ../pyScope

python setup.py install

cd ../sinedon

python setup.py install

cd ../numextension

python setup.py install

cd ../libcv

python setup.py install

cd ../ImageViewer

python setup.py install</pre>

h2.  python-site-package-path: where the installed python

packages went:

Python installer put the packages you installed to its site-packages directory. This

enable all users on the same computer to access them. The easiest way to find where your

installed package is called by python is to load a module from the package using interactive

python command lines like this:

*  Start python command line from shell

<pre>> python</pre>

*  Import a module from the package. Let's try sinedon here. All packages installed

through the above setup.py script should go to the same place.

<pre>python> import sinedon</pre>

*  If the module is loaded successfully, call the module attribute __path__ (two

underscrolls before "path" and two underscrolls after) will return the location of the

module it is loaded from

<pre>python> sinedon.__path__

RETURNS, For example,

python> &lt;module 'sinedon' from '/usr/lib/python2.5/site-packages/sinedon/__init__.pyc'> </pre>

In this case, /usr/lib/python2.5/site-packages/ is your python-site-package-path.

If you go to that directory, you will find all the packages you just installed.

h2.  Configure leginon.cfg:

Leginon can be configured at three levels:

*  A skeleton (default) configuration file is available:

<pre> _<link linkend="package_path">[python-site-package-path]</link>_/Leginon/config/default.cfg</pre>

*  Configurations for all users

<pre> _<link linkend="package_path">[python-site-package-path]</link>_/Leginon/config/leginon.cfg</pre>

Example of the configuration that you should set: (Here we assume your leginon

database is named "dbemdata", and Leginon log into the database as a user named

"usr_object" with no password

set).<pre>[Images]

path: _your_storage_disk_path_/leginon

</pre>

*  Configurations for individual users that overrides the all-user configuration if

exists

<pre> ~/leginon.cfg</pre>

This configuration should include all the minimal configuration above and

additional configuration for individual user for

convenience<pre>[User]

Fullname: _your_name_  #The name you entered in the leginon administration web page. Note that it is case sensitive</pre>

h2.  Names used in the example installation

From this point on, you will need to enter database user names for different

configuration files and settings. These are NOT Leginon user names but what is required by

MySQL database interaction. Consistent names are essential. In the example shown here, the

leginon database is called "dbemdata", the project database is called "projectdata". The

MySQL user name are the same, "usr_object", and in this case without a password.

h2.  Configure sinedon.cfg:

Sinedon is designed to be able to interact with multiple databases. It can be

configured at global or user level.

*  An example configuration file is available at:

<pre>/your_download_area/Leginon-1.6-ALL/sinedon/examples/sinedon.cfg</pre>

*  Configurations for all users should be placed at the following path

<pre>  _<link linkend="package_path">[python-site-package-path]</link>_/sinedon/sinedon.cfg</pre>

*  Modify host,db,user,passwd to what is used. Note that the user here is MySQL user

Leginon uses to communicate with the database for all Leginon users. For Leginon that

uses Project database, set the following:

<pre>[global]

host: _your_database_host_

user: usr_object

passwd:

[projectdata]

db: projectdata

[leginondata]

db: dbemdata

</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. Database Server-side Installation

The following is for the computer that hosts the databases. This involves installing MySQL

server and creation/configuration of the leginon and project databases.

|_.Name:|_.Download site:|

|MySQL-Server 5.0 or higher|"http://www.mysql.com":http://www.mysql.com|

|MySQL-Client 5.0 or higher|"http://www.mysql.com":http://www.mysql.com|

h2.  MySQL

*  Install MySQL-Server

*  Use your package installer (yum, zypper, YaST) if available.

OR

*  Download the latest MySQL-server RPM for Linux from "www.mysql.com":http://www.mysql.com

*  Install the MySQL-server rpm:

<pre> rpm -Uvh MySQL-server-5.0.xx-y.i386.rpm</pre>

(substitute correct version numbers)

*  Install MySQL-Client

*  Use your package installer (yum, zypper, YaST) if available.

OR

*  Download the latest MySQL-client RPM for Linux from "www.mysql.com":http://www.mysql.com

*  Install the MySQL-client rpm:

<pre> rpm -Uvh MySQL-client-5.0.xx-y.i386.rpm</pre>

(substitute correct version numbers)

*  MySQL configuration file is usually located in /usr/share/mysql. There are

several examples there:

<pre>&gt; ls /usr/share/mysql/my*

/usr/share/mysql/my-huge.cnf

/usr/share/mysql/my-innodb-heavy-4G.cnf

/usr/share/mysql/my-large.cnf

/usr/share/mysql/my-medium.cnf

/usr/share/mysql/my-small.cnf

&gt; </pre>

*  Configure my.cnf in /etc using my-huge.cnf as the template

* <pre>> cp /usr/share/mysql/my-huge.cnf /etc/my.cnf</pre>

*  Edit /etc/my.cnf to add or change query cache variables like these:

<pre>query_cache_type= 1

query_cache_size = 100M

query_cache_limit= 100M</pre>

*  start MySQL Server

<pre> &gt;/etc/init.d/mysqld start</pre>

on some installation,

<pre> &gt;/etc/init.d/mysql start</pre>

For future reference: start | stop | restart MySQL Server with similar

commands:

<pre> &gt;/etc/init.d/mysqld start

>/etc/init.d/mysqld stop

&gt;/etc/init.d/mysqld restart</pre>

If you want to start MySQL automatically at boot on SuSE

<pre> SuSE &gt;chkconfig mysql on

</pre>

*  For future reference, the database location will be:

<pre>&gt; cd /var/lib/mysql

Directory: /var/lib/mysql

> ls

yourdbserver.pid

ib_logfile0

mysql

mysql.sock

test

&gt; </pre>

*  Create leginon database, here we call <link linkend="db_example_names"

>dbemdata</link>

<pre> &gt;mysqladmin create dbemdata</pre>

*  Create project database, here we call <link linkend="db_example_names"

>projectdata</link> (optional)

<pre> &gt;mysqladmin create projectdata</pre>

*  Connect to mysql db

<pre>&gt;mysql mysql

mysql> select user, password, host from user;

+------+----------+-----------+

| user | password | host      |

+------+----------+-----------+

| root |          | localhost |

| root |          | host1     |

|      |          | host1     |

|      |          | localhost |

+------+----------+-----------+

4 rows in set (0.00 sec)</pre>

*  Create and grant privileges to a user called <link linkend="db_example_names"

>usr_object</link> for the databases on both the localhost and other hosts involved.

For example, use wild card '%' for all hosts. You may also set specific privilege to

the user. See MySQL Reference Manual for details

<pre>mysql&gt; create user usr_object@'localhost';

mysql> grant all privileges on dbemdata.* to usr_object@'localhost';

mysql&gt; grant all privileges on projectdata.* to usr_object@'localhost';</pre>

Similarly,

<pre>mysql&gt; create usr_object@'%';

mysql> grant all privileges on dbemdata.* to usr_object@'%';

mysql> grant all privileges on projectdata.* to usr_object@'%';

</pre>

*  Change Root passworld

<pre>mysql&gt; update user set password=password('_a passwd_') where user="root";

Query OK, 2 rows affected (0.01 sec)

Rows matched: 2  Changed: 2  Warnings: 0

mysql&gt;^D or exit;</pre>

From now on, you will need to specify the password to connect to the database as

root user like this:

<pre>>mysql -u root -p mysql</pre>

<emphasis role="bold">***If your password change does not take effect in your next

database connection, you will need to flush the mysql pivileges cache as mysql root

and connecting with you old password (or no password in the above

case):</emphasis>

<pre>>mysql -u root mysql</pre>

<pre>mysql&gt; flush privileges;

mysql&gt;^D or exit;</pre>

*  Check MySQL variables

<pre>&gt;mysql -u usr_object dbemdata

mysql> SHOW VARIABLES LIKE 'query%';

+------------------------------+-----------+

| Variable_name                | Value     |

+------------------------------+-----------+

| ft_query_expansion_limit     | 20        |

| have_query_cache             | YES       |

| long_query_time              | 10        |

| query_alloc_block_size       | 8192      |

| query_cache_limit            | 104857600 | <<---This should correspond to your change

| query_cache_min_res_unit     | 4096      |

| query_cache_size             | 104857600 | <<---This should correspond to your change

| query_cache_type             | ON        | <<---This should correspond to your change

| query_cache_wlock_invalidate | OFF       |

| query_prealloc_size          | 8192      |

+------------------------------+-----------+

10 rows in set (0.00 sec)

mysql&gt; exit;</pre>

*  Make sure MySQL is running

<pre>prompt:~&gt; mysqlshow

+--------------+

| Databases    |

+--------------+

| mysql        |

| dbemdata     |

| projectdata  |

+--------------+</pre>

*  Or check with the following php script (if already installed)

<pre>&lt;?

mysql_connect('your_host.your_institute.edu', 'usr_object', '','dbemdata');

echo mysql_stat();

?&gt; </pre>

Output

<pre> Uptime: 1452562 Threads: 1 Questions: 618 Slow queries: 0 Opens: 117 Flush tables: 1 Open tables: 106 Queries per second avg: 0.000</pre>

h2.  Web server set up and Installation

The following applies to the computer that will host the web-accessable image viewers ( a

part of dbem tools) and project manager (a part of project tools).

h2. Differences between Linux flavors

Different Linux flavors often put web server and mysql-related files in different

locations. This can be confusing. From experience, we found the equivalent on CentOS vs

SuSE. Here we list them for reference. If your system use a different naming and you are

willing to share your experience, please send us the list. We will add it here:

|_.File or Command Head|_.CentOS|_.SuSE|

| php.ini|/etc/| /etc/php5/apache2/|

| httpd.conf|/etc/httpd/conf/|/etc/php5/apache2/|

| default document_root|/var/www/html/|/srv/www/htdocs/|

| apache start/stop/restart command head|/etc/init.d/httpd|/etc/init.d/apache2|

| mysql start/stop/restart command head|/etc/init.d/mysqld|/etc/init.d/mysql|

h2. Prerequisites for dbemtools, projecttools, and mrctools extension

The dbemtools are mostly php scripts that run at the web server. The followings are

required before installation of dbemtools and the mrc extension that handles mrc files to be

displayed. Some of these packages may be found on the SuSE Linux DVD or included in common

package repository. MySQL and the Apache Web Server can be downloaded from their respective

websites.

|_.Name:|_.Download site:|_.yum package name|_.SuSE rpm name|

| Apache|"www.apache.org":http://www.apache.org| httpd| apache2|

| php|"www.php.net":http://www.php.net| php| php|

| php-devel*|"rpmfind.net/linux/RPM/Development_Languages_PHP.html":http://rpmfind.net/linux/RPM/Development_Languages_PHP.html| php-devel| php-devel|

| php-gd (including GD library, its development libraries and header *)|"www.php.ned/gd":http://www.libgd.org(Use gd2)| php-gd, gd-devel| php-gd,gd-devel|

| fftw3 library (including development libraries and header *)|"www.fftw.org":http://www.fftw.org(Use fftw3.x)| fftw3-devel| fftw3-devel|

* mrctools are compiled and added to php extension with php-devel package. Mrctools use

GD and FFTW3 that need to be compiled from their development libraries while the extension

is compiled. If GD and FFTW3 sources were downloaded and compiled directly on your computer,

these development files are included. If (as in most cases) GD and FFTW3 are installed from

rpm, they are not included. An error message will appear when you attempt to compile

mrctools. In this case, you will need separate download and installation of GD-devel and

FFTW3-devel. Search "http://rpmfind.net/linux/rpm2html/":http://rpmfind.ned/linux/rpm2html/for GD-devel and FFTW3-devel for the rpm

distribution needed for your system.

h2. Installation tools

Use the installation tools available for your linux distribution.

*  For example, Use yum utility to install.

*  For example, Use the SuSE Linux YaST2 utility or zypper (openSuSE 10.2 and above)

to install.

* "A list of required CENTOS

rpms and instruction":http://emg.nysbc.org/bb/viewtopic.php?t=238can be found at dbemtools bulletin board at

leginon.org.

h2.  PHP, PHP-devel, gd, and fftw3

Install the packages using your installation tools if available. For example, to

install gd as php extension you may use

<programlisting>CentOS> yum install php-gd

SuSE10.2 and above> zypper install php-gd</pre>

h2.  Configure php.ini

Edit the following two sections in php.ini (found as /etc/php.ini on CentOS and

/etc/php5/apache2/php.ini on SuSE) so that they look like the following:

<pre>register_argc_argv = On</pre>

<pre>short_open_tag = On</pre>

<pre>max_execution_time = 300     ; Maximum execution time of each script, in seconds

max_input_time = 300     ; Maximum amount of time each script may spend parsing request data

memory_limit = 256M      ; Maximum amount of memory a script may consume (8MB)</pre>

You may want to increase max_input_time and memory_limit if the server is heavily used.

At NRAMM, max_input_time=600 and memory_limit=4000M.

h2.  Apache Web Server

*  Install the Apache Web Server with the YaST or yum utility.

*  Find "httpd.conf".

This is /etc/httpd/conf/httpd.conf on CentOS and /etc/php5/apache2/httpd.conf on

SuSE

*  Edit the "httpd.conf" configuration file to look like the following:

<pre>&lt;IfModule mod_dir.c&gt;

DirectoryIndex index.htm index.shtm index.html index.shtml index.php

&lt;/IfModule&gt;</pre>

(Note: It may be possible to edit httpd.conf in YaST2 as well.)

*  Restart the web server.

<pre>apachectl restart

or

/etc/init.d/httpd restart     (ON CentOS)

or

/etc/init.d/apache2 restart   (ON SuSE)</pre>

If you want to start the web server automatically at boot on SuSE

<pre> SuSE &gt;chkconfig apache2 on

</pre>

h2. Check php information

Create the following info.php in your web server document root directory (/var/www/html

on CentOS. /srv/www/htdocs on SuSE. You can find its location in httpd.conf mentioned above

under the line starting

DocumentRoot).<pre>&lt;?php

phpinfo();

?&gt;</pre>

Visit this page at http://yourhost/info.php

You will see comprehensive tables of php and apache information, including the location

of the addition .ini files, extension, include path, and what extension is enabled.

Here is an example screen shot of the part of the info.php page that tells you where

php.ini and other configuration files are.

<graphic fileref="http://emg.nysbc.org/software/leginon/images/images/phpini.png"

format="PNG"/>

h2.  mrctools Installation

mrctools are installed as php extension and are required for displaying mrc files live

on the web browser.

h2.  Install php-devel packages on the web server if missing:

You can check whether php-devel is installed by

typing<pre> &gt;phpize</pre>

Follow the instruction for your specific Linux distribution.

For example, SUSE users can use YaST or zypper to install them

h2.  php-GD/FFTW3-devel

Follow instructions from the download site. These may be included already. If not,

mrctools installation will fail.

h2.  mrctools Installation

mrctools are installed from php devel directory. This is usually /usr/include/php/ext

where you will find other php extension source such as gd. After the installation, mrc.so

should be placed in php's extension directory (Look for "extension_dir" in

http://your_host/<link linkend="install_infophp">info.php</link>

*  Download dbem tools from "http://emg.nysbc.org/software/mrctools":http://emg.nysbc.org/software/mrctools.

*  Follow the instruction at "http://emg.nysbc.org/software/mrctools/mrc_so.php":http://emg.nysbc.org/software/mrctools/mrc_so.phpfor installation and

testing. The next session about checking php information can also help debugging the

installation

h2.  Check php information

Visit or refresh http://yourhost/info.php <link linkend="install_infophp">which you

created earlier</link>. It should have a section looking like this (The version should

correspond to what you've just installed):

<graphic fileref="http://emg.nysbc.org/software/leginon/images/images/phpmrc.png"

format="PNG"/>

If mrc is not listed, the extension did not get added at the right order.

h2.  Alternative approach if mrc module does not show up in info.php output

* find in the <link linkend="install_infophp">info.php web page</link> the location

of "additional .ini files parsed" in the first table (such as

/etc/php.d/conf.d/*).

*  Go to the directory and make a copy of any ini file to use as a template for

mrc.ini

<pre>&gt;cd [additional_ini_directory]

&gt;cp gd.ini mrc.ini</pre>

*  Edit mrc.ini to the following

<pre>; comment out next line to disable mrc extension in php

extension=mrc.so</pre>

*  Comment out mrc extension from php.ini (found in /etc/php.ini/ on a typical PHP

installation)

<pre>;extension=mrc.so</pre>

*  restart your webserver

<pre>&gt; /etc/init.d/httpd restart</pre>

h2.  Web Viewing Tools (dbemtools) Linux

Installation

php and java scripts for viewing images and Leginon information through the web

server.

*  Download dbem tools from "http://emg.nysbc.org/software/dbemtools":http://emg.nysbc.org/software/dbemtools.

*  Unpack the package in your [webdirectory]

<pre>&gt;cd [webdirectory]			#/var/www/html in this example

[webdirectory&gt;tar zxvf dbem_1_5_1.tgz</pre>

*  Copy config.php.template to config.php and edit the latter by adding these MySQL

parameters:

"config.php" should be located in /var/www/html/dbem_1_5_1/ on CentOS and

/srv/www/htdocs/dbem_1_5_1/ on SuSE.

<pre>&lt;?

// ---define dbem web tools base ---//

define('BASE_URL',"/dbem_1_5_1/";

// --- Leginon Viewer Configuration --- //

// --- Set your leginon MySQL database server parameters

$DB_HOST    = "[your database host]";

$DB_USER    = "<link linkend="db_example_names">usr_object</link>";

$DB_PASS    = "";

$DB        = "<link linkend="db_example_names">dbemdata</link>";

// --- XML test dataset

$XML_DATA = "test/viewerdata.xml";

// --- Project database config

$PROJECT_URL = "/project_1_2";

$PROJECT_DB_HOST = "[your database host]";

$PROJECT_DB_USER = "<link linkend="db_example_names">usr_object</link>";

$PROJECT_DB_PASS = "";

$PROJECT_DB = "<link linkend="db_example_names">projectdata</link>";

</pre>

*  Test the set-up by visiting http://yourhost/dbem_1_5_1

h2.  Project management tools Linux Installation

Leginon sessions can be catagorized into different projects. The projects are created

and viewed trhough a set of web tools. To access them, install the tools on the web server.

The same project management tools are also used to create and track appion processing

databases. If you want to use our processing pipeline, Appion, in the future, you must

install this.

h2. Prerequisites for project tools