Differences between revisions 4 and 58 (spanning 54 versions)
Revision 4 as of 2010-03-29 08:26:09
Size: 2453
Editor: root
Comment:
Revision 58 as of 2013-06-27 06:59:34
Size: 2985
Editor: IanRees
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
= EMEN2/Install = = Installing and configuring EMEN2 =
Line 3: Line 3:
Generally, you will want to create a user account for running emen2, e.g. 'emen2.' This has the benefit of working well with the default config file. Running as any other user also works fine, you will just have to change one or two paths in config.yml. EMEN2 has a number of dependencies, which are described on the [[EMEN2/Dependencies|dependencies]] page. However, because EMEN2 is often used with [[EMAN2]], we have packaged all of the EMEN2 dependencies along with binary builds of EMAN2, which greatly simplifies installation. See the [[EMAN2]] page for information on installing EMAN2 and the notes below. On Linux, we usually install EMAN2 into $HOME/EMAN2; make sure to run the "EMAN2/eman2-installer" script and add the resulting EMAN2 init script (EMAN2/eman2.bashrc) to your shell rc (usually $HOME/.profile or $HOME/.bashrc).
Line 5: Line 5:
1. Download the latest EMEN2 source code release and untar '''Note:''' After reading this document, you can view a [[EMEN2/Install/Example|walk-through of a successful installation]].

= Install EMEN2 =

EMEN2 can be installed using either Python easy_install:
Line 8: Line 12:
cd /home/emen2
tar -xvzf emen2.03.28.2010.tar.gz
cd emen2
sudo python -m easy_install -U emen2
Line 13: Line 15:
2. Create a directory for the Database Environment (referred to as $DB_HOME going forward. Reasonable default is /home/emen2/db/ ) Note the "-U" flag will upgrade emen2 to the current version if it is already found.

Alternatively, you may install EMEN2 by downloading the source, unpacking, and running the setup.py script:

[[http://pypi.python.org/pypi/emen2|Download EMEN2]]
Line 16: Line 22:
mkdir /home/emen2/db
cp config/config.sample.yml /home/emen2/db/config.yml
python ./setup.py build
sudo python ./setup.py install
Line 20: Line 26:
Recommended: Set the $DB_HOME environment variable to this path for convenience. Place this in your .bash_profile or similar. '''Note:''' Installing EMEN2 with EMAN2

If you are using an EMAN2 binary distribution to take care of all the dependencies, you will need to use EMAN2's Python environment on Linux and Windows. On Linux, assuming you installed EMAN2 into $HOME/EMAN2, you would use $HOME/EMAN2/Python/bin/python as the interpreter. This will ensure that the correct dependencies are loaded and EMEN2 is installed in the correct location. On Mac OS X, EMAN2 uses the system default Python environment, so no special action is required. Example:
Line 23: Line 31:
export DB_HOME=/home/emen2/db $HOME/EMAN2/Python/bin/python -m easy_install -U emen2
Line 26: Line 34:
3. Copy emen2/config.sample.yml to $DB_HOME/config.yml = Creating an EMEN2 database environment =
Line 28: Line 36:
Edit the various settings in config.yml. See [[EMEN2/config.yml]]. Primarily, you will want to check the path and network settings. A simple configuration will have most EMEN2 directories (db, applog, archive, db_hotbackup, emen2files, etc.) placed under the path specified by the "&root" element, which is /home/emen2/ by default. Here is a "quick start" guide to initialize an EMEN2 DB and start the web server. The "-h" argument in the scripts below are references to a directory to keep the EMEN2 DB; the directory will be created if it does not exist.
Line 31: Line 39:
  root: &root
    /home/emen2/
python -m emen2.db.create -h $HOME/test.db
Line 35: Line 42:
4. After config.yml is to your liking, run This will prompt for a "root" account password, and create a minimal EMEN2 environment. The email address will be used for password recovery and system messages if a mail server is provided in the configuration. The password can be left empty, but the system will not be secure at all.

To start the EMEN2 web server with default settings:
Line 38: Line 47:
python ./setup.py python -m emen2.web -h $HOME/test.db
Line 41: Line 50:
The rest of the $DB_HOME environment will be created, skeleton parameter/protocol definitions will be installed, and a root user created. You will be prompted on the shell for a root password. You will be able to access the server at http://localhost:8080
Line 43: Line 52:
5. Test web server Another way to start the web server is to use the "[[EMEN2/emen2ctl|emen2ctl]]" program:
Line 46: Line 55:
python ./TwistSupport.py emen2ctl restart -h $HOME/test.db
Line 49: Line 58:
You should be able to connect to this web server instance once it is "listening..." The default port is 8080. You may login with the root password you specified previously. This will daemonize emen2, and log all messages to a file, $HOME/test.db/log/emen2.log.
Line 51: Line 60:
6. Optional: Import Parameter/Protocol definitions from the NCMI Database.

{{{
python ./clients/clone.py -- --defs
}}}

Note: the first "--" is intentional and required at the moment. Command arguments for the local database go before "--", arguments to the cloning script go after ("--defs")

You will be prompted for two sets of credentials. First, an NCMI DB account, and second, the root password for the local database. If you do not have an NCMI DB account, you may specify "anonymous" as the username, and your email address as the password.

6. Daemon

After you are satisfied with your setup, you can run EMEN2 in the background

{{{
python ./emen2control.py --start
}}}
Finally, if you want to start EMEN2 at system boot, see [[EMEN2/Startup|EMEN2 Startup]] for details on using the [[EMEN2/emen2ctl|emen2 init script]].

Installing and configuring EMEN2

EMEN2 has a number of dependencies, which are described on the dependencies page. However, because EMEN2 is often used with EMAN2, we have packaged all of the EMEN2 dependencies along with binary builds of EMAN2, which greatly simplifies installation. See the EMAN2 page for information on installing EMAN2 and the notes below. On Linux, we usually install EMAN2 into $HOME/EMAN2; make sure to run the "EMAN2/eman2-installer" script and add the resulting EMAN2 init script (EMAN2/eman2.bashrc) to your shell rc (usually $HOME/.profile or $HOME/.bashrc).

Note: After reading this document, you can view a walk-through of a successful installation.

Install EMEN2

EMEN2 can be installed using either Python easy_install:

sudo python -m easy_install -U emen2

Note the "-U" flag will upgrade emen2 to the current version if it is already found.

Alternatively, you may install EMEN2 by downloading the source, unpacking, and running the setup.py script:

Download EMEN2

python ./setup.py build
sudo python ./setup.py install

Note: Installing EMEN2 with EMAN2

If you are using an EMAN2 binary distribution to take care of all the dependencies, you will need to use EMAN2's Python environment on Linux and Windows. On Linux, assuming you installed EMAN2 into $HOME/EMAN2, you would use $HOME/EMAN2/Python/bin/python as the interpreter. This will ensure that the correct dependencies are loaded and EMEN2 is installed in the correct location. On Mac OS X, EMAN2 uses the system default Python environment, so no special action is required. Example:

$HOME/EMAN2/Python/bin/python -m easy_install -U emen2

Creating an EMEN2 database environment

Here is a "quick start" guide to initialize an EMEN2 DB and start the web server. The "-h" argument in the scripts below are references to a directory to keep the EMEN2 DB; the directory will be created if it does not exist.

python -m emen2.db.create -h $HOME/test.db

This will prompt for a "root" account password, and create a minimal EMEN2 environment. The email address will be used for password recovery and system messages if a mail server is provided in the configuration. The password can be left empty, but the system will not be secure at all.

To start the EMEN2 web server with default settings:

python -m emen2.web -h $HOME/test.db

You will be able to access the server at http://localhost:8080

Another way to start the web server is to use the "emen2ctl" program:

emen2ctl restart -h $HOME/test.db

This will daemonize emen2, and log all messages to a file, $HOME/test.db/log/emen2.log.

Finally, if you want to start EMEN2 at system boot, see EMEN2 Startup for details on using the emen2 init script.

EMEN2/Install (last edited 2013-06-27 06:59:34 by IanRees)