---------------------------- README.piana_requirements ---------------------------- This file describes the requirements (software, patches, environment variables, ...) that you need to respect in order to run piana ------------------------------------------------------------------- If you are reading this, it means you have either downloaded it from our web site or checked out a piana cvs version. Good for you! You probably want your system administrator to make sure you comply with the following requirements. Some of these actions must be done as root. If you are installing PIANA it is recommended to read as well README.piana_installation Some people encounter problems when trying to respect the requirements: if you are experienced with LINUX, you'll have no trouble at all. If not... good luck! If even with good luck you don't manage to install PIANA, try sending us an email: boliva at imim.es ------------------------------------------------------------------ *********************************** 1. Operating System and Hard Drive *********************************** PIANA has been tested on LINUX Fedora Core 2, Debian Linux and MAC OS X Tiger (see notes at the end of this file for MAC OS X installation). It should also work on all other *NIX platforms. Since everything is written in python, it shouldn't be too difficult to use it under other operating systems, as long as you can install the other programs and modules PIANA requires. The space taken by PIANA code on your hard drive is very small, just a few MBs. However, for the PIANA database you will need more space: - If you are going to use the PIANA database we provide on our webpage, the machine with the mysql server must have at least 6 GB - If you are going to create the PIANA database with the parsers we provide, you can control how big your database will be by parsing only the data you are really interested in. Our local copy of the PIANA database takes almost 8GB of disk space. ***************************** 2. External software required ***************************** These external software (programs & python modules) must be installed on your computer in order to run piana. Some of them are already installed by standard Linux distributions; others aren't. Make sure you have all of them. -------------------------------- 2.1 EXTERNAL PROGRAMS TO INSTALL -------------------------------- First of all, you need to install 'python' and 'mysql'. --> python must be installed on the machine that is going to run piana (It is already installed in most standard distributions) --> mysql client must be installed on the machine that is going to run piana --> mysql server must be installed on the machine that is going to hold the piana database --> both machines can be the same (ie. piana code and piana database can be on the same machine) (Versions higher than the one written below should also be compatible with PIANA: if you are going to install these on your system, choose the latest versions of each program) - Python 2.3: http://www.python.org/download/ (python development and headers also needed) - Mysql 4.1 client: http://dev.mysql.com/downloads/ (install client, libraries and headers on the machine that will hold the piana code) - Mysql 4.1 server: http://dev.mysql.com/downloads/ (install server, libraries and headers on the machine that will hold the piana database ) -------------------------------------- 2.2 EXTERNAL PYTHON MODULES TO INSTALL -------------------------------------- These are the external python modules that you'll need to run PIANA. Python modules are easily installable: follow instructions on their websites. (Versions higher than the one written below should also be compatible with PIANA) - MySQL-Python 1.2.0: http://sourceforge.net/projects/mysql-python - numarray: http://www.stsci.edu/resources/software_hardware/numarray (numarray needed! scycore is not supported) - Biopython 1.2: http://www.biopython.org/download/ - cytoscape: http://www.cytoscape.org (only needed if you want to create images of networks from SIF files) - graphviz: http://www.graphviz.org/Download..php (only needed if you want to create images of networks from DOT files) --> It is very important to make sure that all python packages are installed under directory site-packages of the python version you will be using (eg. /usr/lib/python2.3/site-packages) or, in case of installing them on other directories, to make sure the PYTHONPATH enviroment variable correctly points to the packages. --> It is very important that the python version you install for PIANA is the same as the one that is aliased by the system as 'python'. Otherwise, some of the following operations might not work ************************ 3. ENVIRONMENT VARIABLES ************************ python needs to know where the PIANA files are located. In order to do show, you must create (or modify) your PYTHONPATH environment variable. All PIANA directories with code must be added to PYTHONPATH. If you do not know how to do it, you should read README.pythonpath Then, you'll need to make effective these additions: - if you use tcsh: $> source .cshrc - if you use bash: $> source .bashrc *********************************************************** 4. OTHER REQUIREMENTS (PIANA developers and advanced users) *********************************************************** (Only for PIANA developers and PIANA advanced users: standard PIANA users can skip this section. To learn more about the different types of users that PIANA admits, read section "PIANA types of users" in file README.piana_tutorial) 3.1 ==> Standard PIANA users can skip this step In case you are going to use PIANA as a developer (or as an advanced user), you'll need to do the following: install F2PY: http://cens.ioc.ee/projects/f2py2e/ Transform fortran code (fgraph.f) to python readable code $> cd piana/code/Graph $> f2py -c -m fgraph fgraph.f Troubleshotting: --> you need a fortran compiler to do this (eg. g77) --> you might encounter problems doing this if your system is using a python version different from python version you installed for PIANA -> check the path to the f2py that has been installed for the python installed for PIANA (eg. /usr/local/bin/f2py2.3) -> do /usr/local/bin/f2py2.3 -c -m fgraph fgraph.f --> you might encounter problems doing this due to the fortran compiler used by your system. --> check the path for your fortran77 compiler (eg. /usr/bin/g77) --> do 'f2py --fcompiler-exec=/usr/bin/g77 -c -m fgraph fgraph.f' and it will work fine 3.3 ==> Standard PIANA users can skip this step In case you are going to use PIANA as a developer (or as an advanced user), you'll need to do the following: install the following packages: - plplot: http://plplot.sourceforge.net ********************* 5. CODE MODIFICATIONS ********************* This modification is only required if you are going to insert new protein sequences into a piana database As root, you need to change 3 files of the biopython package: $> cp piana/code/utilities/modified_ProtParam.py python2.X/site-packages/Bio/SeqUtils/ProtParam.py $> cp piana/code/utilities/modified_IsoelectricPoint.py python2.X/site-packages/Bio/SeqUtils/IsoelectricPoint.py $> cp piana/code/utilities/modified_SProt.py python2.X/site-packages/Bio/SwissProt/SProt.py For specific details on which are the modifications (and why do we change them) to these files, read /piana/code/utilities/README.modified_biopython_files ****************** 6. TROUBLESHOOTING ****************** If you encounter problems during the installation, you should read section INSTALLATION on README.troubleshooting If you don't manage to install PIANA, you can try sending us an email to boliva at imim dot es ---------------------------------------- APPENDIX: installing on MAC OS X Tiger ---------------------------------------- -> set enviroment variable python as indicated on README.pythonpath -> Attention! MAC OS X normally places python on directories different to other UNIX platforms. For example, /Library/Python/2.3 -> install all requirements for PIANA as indicated on README.piana_requirements -> all PIANA external programs and modules can be easily installed on MAC OS X -> install module readline on your computer (not installed by default) -> this is the only point that MAC users must pay special attention to: module readline is not installed by default on your machine! Do as follows to install it: $> curl -s http://www.pycs.net/bbum/2004/1/21/readline.so.gz | gzip -d -c | sudo cat > /Library/Python/2.3/readline.so