Installation
- 1. Supported Operating Systems
- 2. How to Get It
- 3. Environment
- 4. Directory Structure
- 5. Description of Programs
- 6. Installation
- 7. License Key
1. Supported Operating Systems
The executables in the automar distribution have been compiled and are available for the following operating systems:
Name | OS | Version |
---|---|---|
Linux | CentOS, Ubuntu | ≥5.x, ≥ 10.x |
Apple | Mac OS X | 10.10.x Yosemite |
Note: Apple Mac OS X requires X11 (XQuartz) that must be obtained and installed
separately. The programs also rely on MacPorts libraries for X11 to be installed
in /opt/local.
2. How to Get It
The automar distribution is available free of charge from our website at: http://www.marxperts.com/pub/automar/automar.dist.tgz.
Programs that do not belong to marXperts GmbH, i.e. all CCP4 programs including MOSFLM and AIMLESS must be obtained from the CCP4 web site. Programs denzo, scalepack, XDS and XSCALE are are commercial programs and are therefore NOT included within this distribution.
3. Environment
The environment should best be defined within the shell startup scripts, i.e. files $HOME/.cshrc (C-shell) or $HOME/.tcshrc (TC-shell) or $HOME/.bashrc (Bourne-shell) using the usual nomenclature. When executing the installation script (setup), the additions to the corresponding login scripts will be done automatically. This scipt also takes care about the CCP4-environment settings which are needed for the additional programs from the CCP4-suite.
Name | Description |
---|---|
MARPRCDOCDIR | Location of directory tree with documentation. |
MARPRCDATDIR | Directory where to save current session parameters (automar.mix). |
MARPRCDEFDIR | Directory where to find default session parameters (automar.defaults) and executable file cleanup.com |
AUTOMARDOCDIR | Location of directory tree with documentation. Only used if MARPRCDOCDIR is not defined. |
AUTOMARDATDIR | Directory where to save current session parameters (automar.mix). Only used if MARPRCDATDIR is not defined. |
AUTOMARDEFDIR | Directory where to find default session parameters (automar.defaults) and executable file cleanup.com Only used if MARPRCDEFDIR is not defined. |
AUTOMARDIR | Root directory of the automar distribution with subdirectories $AUTOMARDIR/man for the documentation and $AUTOMARDIR/dat containing session files. Only used if others are not defined. |
4. Directory Structure
The automar program suite directory ($AUTOMARDIR) contains the following directories.
Directory | Contents |
---|---|
bin/linux | Binary executables for Linux (RedHat, Ubuntu, etc.) |
bin/osx86 | Binary executables for Mac OS X (Intel) |
ccp4 | Stuff required for defining the environment of CCP4-programs |
man/man | Unformatted man pages for programs written by marxperts |
man/html | HTML conversions of unformatted man pages |
man/css | Style sheets used by HTML pages |
man/layout | Design elements used by HTML pages |
man/automar | HTML documentation of automar program suite |
man/automar/img | Graphics files used by HTML pages |
man/ccp4 | HTML documentation of mosflm and the some CCP4-programs |
dat | Startup file for program automar (automar.mix). |
tmp | Temporary files used by some CCP4-programs |
When installing the automar program suite, make sure to create these directories.
5. Description of Programs
Name | man page | html page | Description |
---|---|---|---|
automar | yes | yes | GUI for data processing |
marPeaks | yes | yes | Spot search in images |
marIndex | yes | yes | Autoindexing |
marPredict | yes | yes | Predicts patterns from matrix of marIndex |
marStrategy | yes | yes | Obtains best data collection strategy |
marProcess | yes | yes | Integrates images |
marPost | yes | yes | Postrefinement and addition of partials |
marScale | yes | yes | Scales and merges data from marProcess-run |
sortmtz/binsort | no | yes | Sorts "mtz"-file from mosflm-run |
aimless | no | yes | Scales and merges data from mosflm-run |
truncate | no | yes | Converts intensities to structure factors |
mar2mtz | no | yes | Converts output from marScale into "mtz"-file |
mtz2various | no | yes | Converts binary "mtz"-files into other formats |
mtzdump | no | yes | Lists contents of binary "mtz"-files |
mtzutils | no | yes | Various data manipulation tools for "mtz"-files |
6. Installation
6.1 Download
- Download the desired tgz-packages from the ftp site
(see above). You should download files:
automar.dist.tgz - Move packages to a new temporary directory, i.e. type:
mkdir $HOME/tmp/new - Go to this directory, i.e. type:
cd $HOME/tmp/new - Untar the gzipped tar file, i.e. type:
tar xvfz automar.dist.tgz - Run the installation script, i.e. type:
automar/automar-install
6.2 Setup
The "automar-install"-installation script is a text based shell script that will ask you a couple of questions. Defaults (in [brackets]) will be applied when just typing return. The default location of the automar program suite should be $HOME/automar.
The "setup"-procedure will modify your login scripts (either .cshrc or .tcshrc) and append the new path names and environment parameters at the end of the file.
After finishing the "setup"-procedure, source the .cshrc or .tcshrc file and start work, e.g. by typing: automar
If for some reasons the automar-install script fails, it is easy enough to do the setup manually. The installation consists of:
- Copying the entire automar distribution to a defined place, e.g. to $HOME/automar.
- Modify the shell scripts initialization files, i.e. file $HOME/.cshrc if you are using csh or tcsh as login shell or $HOME/.bashrc if you are using basgh as login shell.
Example for .cshrc:
setenv AUTOMARDIR $HOME/automar setenv AUTOMARDOCDIR $AUTOMARDIR/man set path = ( $path $AUTOMARDIR/bin/linux/i386 )
Example for .bashrc:
export AUTOMARDIR='${HOME}/automar' export AUTOMARDOCDIR='${AUTOMARDIR}/man' auto='${AUTOMARDIR}/bin/linux/i386' if [ ${PATH} ]; then export PATH="${PATH}:${auto}" else pub=".:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/bin" export PATH="${pub}:${auto}" fi
Some programs out of this software suite make use of a license key mechanism. Please refer to the following section for more details.
7. License Key
As of version 2.8 of automar published in July 2011 the
programs out of automar program suite do NOT require a license file any more.
If your programs still ask for a license, please consider to download the
latest executables from our website:
http://www.marxperts.com/pub/automar/automar.dist.tgz
In case you prefer to continue with your existing executables, please read the
next paragraph.
The automar software suite is NOT public-domain software. marXperts GmbH, however, does NOT charge license fees for the programs contained within this suite, but users must get registered in order to continue using the programs after a compilation-date coupled period of usage has expired.
License keys will be supplied to customers of marXperts GmbH and Rayonix, LLC, only.
The following programs require a license key:
- marPeaks
- marIndex
- marPredict
- marStrategy
- marProcess
- marPost
- marScale
- automar
License keys are platform specific. A license key file must be installed on each computer in order to be able to run the programs.
Run program marlicense on each platform where you want to install the corresponding programs. marlicense is contained within the automar software suite. This program requires simple terminal input and produces an ASCII type output file named "marlicense.hostname" that must be mailed to marXperts GmbH.
marxperts will return a crypted license file that must be installed in one of the following locations on the target host computer.
- 1. /usr/local/mar/marlicense.$HOST
- 2. $HOME/.marlicense.$HOST
- 3. ./marlicense.$HOST (i.e. current directroy)
As a last resort, if there is no license key installed at all
the programs have a limited lifetime coupled to the date of
compilation.