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| = Installation = <<TableOfContents>> === For the impatient === Down load the tarball and unpack: {{{$ tar zxf ScrumPy.tgz}}} Now cd into the freshly created directory then (as root): {{{# python install.py}}} This will create a launcher script - {{{/usr/local/bin/ScrumPy}}} by default - which can be simply run from the command line. |
= Installing ScrumPy = |
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| === OS === We currently use debian/squeeze as our development platform, and if you have the choice this is reccomended as you should then be able to continue in impatient mode. {{{ScrumPy}}} should install on any Linux distribution, possibly after editing the configuration file [[ScrumPy/Doc/InstallConf|install_conf.py]], and probably on most other unix variants. Brief notes for installing on Red Hat derivatives can be found [[ScrumPy/Installation/RedHat|here]] We don't have a Windows version, and we are not currently planning one. If anyone is interested in porting ScrumPy to windows please get in touch. As far as I am aware, there are only two places in the source that would require modification, both of which are concerned with loading shared objects. |
=== Operating Systems === The current version of !ScrumPy can be installed on Debian 8 (Jessie), Ubuntu 1404 (Trusty) or later and Centos 6. Debian 7 (Wheezy) will probably work, but may result in some loss of function and/or require manual intervention, Debian 6 (Squeeze) will only work with a lot of manual intervention and is deprecated. For installation on other Unix-like systems see [[ScrumPy/InstallConf|these notes]] |
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| Python 2.7 is recommended. 2.8 would ''probably'' be OK, but has not yet been fully tested, and may produce verbiage concerning Python 3 issues. Python 3 will almost certainly not (at present) work. | !ScrumPy requires python 2.7 or 2.8. Python 2.6 ''might ''work but is long obsolete and not reccomended. Python 3 is not currently supported. |
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| === SBML === SBML functionality depends on libsbml [[http://sbml.org/Software/libSBML|libsbml]] . This is not distributed as part of ScrumPy, so must be installed separately (''after'' installing {{{ScrumPy}}}). Version 5.5 is reccomended. Later versions will ''probably'' be OK, but haven't yet been tested. When installing libsbml ensure you specify "--with-python" at the configuration stage. You will als need to run "ldconfig" once the installation is complete. |
== Installation == Download the current [[http://mudsharkstatic.brookes.ac.uk/Download/ScrumPy.tgz|tarball]], unpack it and cd into the newly created !ScrumPyXXXX directory (XXXX is the revision number). Then, as root, execute the install.py script. This will install a number of prerequisite packages which may take some time depending on what is already installed. A number of extension C libraries will also be compiled that may take a little time and generate a fair ammount of verbiage on the terminal. As long as the last looks something like: |
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| === Other dependencies === All other dependencies are automatically taken care of by the install script, bit be sure to read the configutation instuctions below. |
{{{ Makefails = [] }}} It can safely be ignored. |
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| == Configuration == === General === Configuration details are held in the file [[ScrumPy/Doc/InstallConf|install_conf.py]]. The default file is suitable for Debian and Ubuntu platforms (and most likely other Debian derivatives). Follow the lik for explanations. |
!ScrumPy will now be installed in /usr/lib/python2.n/dist-packages/ScrumPy, and a start script installed in /usr/local/bin/ScrumPy. !ScrumPy can now be started by simply typeing !ScrumPy at the command line. A few diagnostic messages will appear in the terminal, but these are for information only (see note on SBML below) and not errors. |
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| === Other Options === The install script recognises two additioanl arguments which can appear anywhere on the command line : "NOPKG" and "LIBONLY". |
Further documentation continues [[ScrumPy/Doc/ModEnv#RunSpy|here]]. |
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| If the "NOPGK" argument is given none of the dependent packages will be installed. This will speed things a bit if you know that the packages are in place. Another time at which this might be useful is if you are installing as a non-root user. However, under these circumstances you will need write access in other places (see install_conf). The "LIBONLY" compiles and installs the C extension modules without installing any Python. This is a development/maintaince option only. === Initial testing === The ScrumPy installation script will produce a ''lot'' of verbiage on your terminal, however this mainly reportage/diganostic information related to the compilation of the varous C libraries. If you see explicit errors here, it is most likely due to missing or non-standard development packages. Another possibility is your C compiler is stricter than gcc 4.4.5 currently distributed with Debian-Squeeze. If you do get errors at this point check [[ScrumPy/Doc/InstallConf|install_conf.py]] and if the problem remains unfixable, get in touch. Once installed {{{Scrumpy}}} can be run by simply entering {{{Scrumpy}}} at the command line. You should then see the main {{{ScrumPy}}} window shown below. {{attachment:ScrumPyStart.png||width="600"}} Further doccumentation continues [[ScrumPy/Doc/ModEnv#RunSpy|here]]. |
== SBML support. == !ScrumPy uses libsbml to to read/write sbml format file. If libsbml is present in your distributions repository it will be installed automatically, otherwise libsbml will need to be installed manually from source (with the python option). |
Installing ScrumPy
Prerequisites
Operating Systems
The current version of ScrumPy can be installed on Debian 8 (Jessie), Ubuntu 1404 (Trusty) or later and Centos 6. Debian 7 (Wheezy) will probably work, but may result in some loss of function and/or require manual intervention, Debian 6 (Squeeze) will only work with a lot of manual intervention and is deprecated. For installation on other Unix-like systems see these notes
Python
ScrumPy requires python 2.7 or 2.8. Python 2.6 might work but is long obsolete and not reccomended. Python 3 is not currently supported.
Installation
Download the current tarball, unpack it and cd into the newly created !ScrumPyXXXX directory (XXXX is the revision number). Then, as root, execute the install.py script. This will install a number of prerequisite packages which may take some time depending on what is already installed. A number of extension C libraries will also be compiled that may take a little time and generate a fair ammount of verbiage on the terminal. As long as the last looks something like:
Makefails = []
It can safely be ignored.
ScrumPy will now be installed in /usr/lib/python2.n/dist-packages/ScrumPy, and a start script installed in /usr/local/bin/ScrumPy. ScrumPy can now be started by simply typeing ScrumPy at the command line. A few diagnostic messages will appear in the terminal, but these are for information only (see note on SBML below) and not errors.
Further documentation continues here.
SBML support.
ScrumPy uses libsbml to to read/write sbml format file. If libsbml is present in your distributions repository it will be installed automatically, otherwise libsbml will need to be installed manually from source (with the python option).