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  1. INSTALLATION INSTRUCTIONS FOR MOBYLE
  2. ************************************
  3.  
  4.  
  5. 1 - Requirements:
  6. =================
  7.  
  8. - Any machine running a unix-like Operating System.
  9. - A CGI-enabled web server (such as Apache with a loaded mod_cgi and optionally the rewrite engine).
  10. - Python, >=2.5 & <3.0
  11. - The following Python libraries:
  12.         + simpletal, >= 4.1 & <5.0
  13.         + simplejson, >= 1.7.1
  14.         + python imaging library (with libpng, zlib and freetype support), >= 1.1.5  
  15.         + lxml >=2.2.4 ,
  16.  
  17. (remark: pyCaptcha is not required anymore as it was integrated in Mobyle )
  18.  
  19. - Optional:
  20.         + a biological sequence/alignment format converter software. We recommend squizz
  21.           (ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz-0.99b) and we provide a plugin for it.
  22.         + a batch system, such as SGE (http://gridengine.sunsource.net/), PBS/Torque
  23.           (http://www.clusterresources.com/pages/products/Torque-resource-manager.php), or LSF.
  24.         + python-drmaa http://drmaa-python.googlecode.com/ if you use SGE via DRMAA, PBS/Torque
  25.           via DRMAA, or LSF via DRMAA. We do not provide a non-DRMAA access to Torque or LSF.
  26.         + FedStage DRMAA for LSF (http://sourceforge.net/projects/lsf-drmaa/) if you use LSF
  27.         + if you use Torque/PBS via DRMA enable this option at compilation time.
  28.         + dnspython >=1.5.0 is helpful to check user emails domain validity.
  29.         + golden (ftp://ftp.pasteur.fr/pub/gensoft/projects/golden/) is helpful to directly load
  30.           biological sequences from databanks into the web portal.
  31.         + python-openid >=2.2.4 (http://openidenabled.com/files/python-openid/packages/python-openid-2.2.4.tar.gz)
  32.           to enable OpenId authentication.
  33.         + the service descriptions (ftp://ftp.pasteur.fr/pub/gensoft/projects/Mobyle/)
  34.           are collections of "ready-to-use" service descriptions (programs, workflows, or viewers)
  35.           maintained by the Institut Pasteur.
  36.         + the jing java library and dependencies (http://code.google.com/p/jing-trang/downloads/list)
  37.           in case you want to modify service descriptions or create your own. It is not required
  38.           to operate Mobyle, but provides detailed error messages that can help you create valid
  39.           service descriptions.
  40.          
  41. 2 - Technical overview:
  42. =======================
  43.  
  44. A "Mobyle" server does not run any specific daemon (apart from
  45. the web server). When a user launches a job, it is actually running a cgi that
  46. runs a bioinformatics program in a subprocess. If the subprocess runs
  47. for more than a certain time, it detaches itself, and continues
  48. monitoring the execution until its end. The "web server user" is therefore
  49. the one that runs every request and user permissions should be done so
  50. that it can access and run every data, program, and parameter of the
  51. Mobyle configuration.
  52.  
  53. 3 - The Mobyle archive tree:
  54. ============================
  55.  
  56. Doc => Documentation
  57.  
  58. Example => A few sample files.
  59.  
  60. Local => Configuration, local parameters and code for the Mobyle
  61.          system.
  62.  
  63. Schema => The schema files that define the XML data model and the validation
  64.          rules for service descriptions.
  65.  
  66. Src => Mobyle source code:
  67.         * the Mobyle folder contains the "core" code for the Mobyle
  68.           Server.
  69.         * the Portal folder contains the code for the web portal that
  70.           provides an access to the system.
  71.  
  72. Tools => A few utilities and scripts.
  73.  
  74. niad => (only if you choose a Mobyle+BCBB tarball) root of 2 mobyle companion:
  75.   * BCBB Mobyle Interface Designer (BMID)
  76.   * BCBB Mobyle Pipeline System (BMPS)
  77.  
  78. 4 - Installation steps:
  79. =======================
  80.  
  81. 4.1 - Make sure every required dependence/software is present.
  82. --------------------------------------------------------------
  83.  
  84. 4.2 - Perform the installation.
  85. -------------------------------
  86.  
  87. To install Mobyle, you need to provide 3 different paths, where all
  88. files will be installed, and 2 flags to install BMID and BMPS (these 2 flags are only
  89. available if you download a Mobyle+BCBB tarball) :
  90.  
  91.     python setup.py install \
  92.       --install-core=/path/where/to/install/core/files \
  93.       --install-cgis=/path/where/to/install/cgis/files \
  94.       --install-htdocs=/path/where/to/install/html/files
  95.       --install-bmps    
  96.       --install-bmid
  97.      
  98.   - The `--install-core' option specifies the directory where to install the Mobyle
  99.     core files (code, tools, example, documentation, ...).
  100.  
  101.   - The `--install-cgis' option specifies the directory where to install the Mobyle
  102.     portal cgis to be executed by the web server.
  103.  
  104.   - The `--install-htdocs' option, will be used as the Mobyle document
  105.     root, which will contain the portal static documents (in a 'portal' subfolder),
  106.     the users sessions, the jobs and the programs definitions (in a 'data'
  107.     subfolder). Make sure this subtree is readable by the web server
  108.     user. Furthermore, the permissions on subfolders 'sessions' and
  109.     'jobs' have to be writable by Apache.
  110.    
  111.    - The --install-bmps flag, indicate that the installer will install BMPS,
  112.      the BCBB Mobyle Pipeline System. BMPS will be installed in Mobyle cgis location.
  113.      (this option is available for Mobyle+BCBB tarball only).
  114.      
  115.    - The --install-bmid flag, indicate that the installer will install BMID,
  116.      the BCBB Mobyle Interface Designer. BMID will be installed in Mobyle cgis location.      
  117.      (this option is available for Mobyle+BCBB tarball only).
  118.      
  119. 4.3 - Configure Mobyle and Apache.
  120. ----------------------------------
  121.  
  122. Go to your freshly installed "Mobyle core" directory (from now on, you can remove
  123.  the sources), and create the configuration file using the provided template:
  124.  
  125. cp Example/Local/Config/Config.template.py  Local/Config/Config.py
  126.  
  127. In order to have a working installation, you need to edit the various configuration directives.
  128. The documentation describing the configuration of Mobyle and Apache is the configuration manual
  129. Doc/Admin/how_to_configure_mobyle.pdf.
  130.  
  131. 4.4 - Services descriptions deployment.
  132. ---------------------------------------
  133.  
  134. The deployment of services using Mobyle does not install the programs, it just makes them
  135. accessible on the web. You must install separately the bioinformatics software corresponding
  136. to the descriptions.
  137.  
  138. We provide a set of "ready-to-use" services descriptions (programs, workflows, viewers), which
  139. are available in the following ftp website: ftp://ftp.pasteur.fr/pub/gensoft/projects/Mobyle/.
  140. For Mobyle 1.0, use Programs-1.3.tgz or higher. Workflows and Viewers are new to version 1.0.
  141.  
  142. For instance, to deploy pasteur-provided program descriptions:
  143.   - download the "Programs-xx.tgz" file,
  144.   - expand the archive in the Programs subfolder,
  145.   - configure Mobyle according to the bioinformatics software installed on
  146.     your platform (see LOCAL_DEPLOY_* directives in the configuration manual),
  147.   - use the mobdeploy script which is located in the Tools subfolder (for more details see associated
  148.     README).
  149.      
  150. Make sure, once the programs descriptions are deployed, that they are readable by the web server.
  151. For more explanations about services deployment see the associated Tools/README file and the
  152. configuration manual.
  153.  
  154. 5 - Tests and troubleshoot:
  155. ===========================
  156.  
  157. Try to connect to your portal. The url of the portal is:
  158.     ROOT_URL/CGI_PREFIX/portal.py
  159.  
  160. You should see the welcome page at the center and, on left, the
  161. available programs presented in a hierarchical tree.
  162.  
  163. If you have any trouble, it will be very useful to check :
  164.  - the apache error log, if you have a "500 Internal Server Error"
  165.  - the Mobyle error_log (located in previously the LOGDIR configuration directive),
  166.    if something seems goes wrong but there is no error 500.
  167.  
  168. Here are a few frequent problems that can occur:
  169.  
  170. * Instead of the welcome page I see 'Internal Server Error'.
  171.     -> Make sure the web server has the writable permissions on the
  172.        --install-htdocs /sessions subfolder.
  173.  
  174. * I do not see the installed services appear in the left menus and/or their forms.
  175.     -> Make sure the files in data/programs/ are readable the web server user.
  176.  
  177. * After filling the CAPTCHA, the Portal freezes:
  178.     -> Check the Mobyle error log for an "IOError: decoder jpeg not available" message.
  179.     If so, the PIL package was not compiled with jpeg support. You must have libjeg installed
  180.     before to install PIL. Check if the PIL install script detects your libjpeg, PIL shows a
  181.     summary after building (python setup.py build_ext -i).
  182.  
  183. * After launching a job, I have : Mobyle Internal server error.
  184.     -> Check the Mobyle error log for an "AsynchronRunner : CRITICAL ... __init__: exec child
  185.     caught an error" message. If you find it, make sure the python module Src/Mobyle/RunnerChild.py
  186.     is executable by the web server user.
  187.  
  188. If your problem is not among those covered above then please contact
  189. us at mobyle-support@pasteur.fr.
  190.  
  191. 6 - Mailing list:
  192. =================
  193.  
  194. There is a mailing list dedicated to Mobyle server administrators, called
  195. "mobyle-users". This list discusses new releases, related software announcements,
  196. administration and development issues, etc. This is a moderated and low traffic list.
  197.  
  198. You can subscribe to Mobyle users at:
  199.     http://sympa.pasteur.fr/wws/subrequest/mobyle-users
  200.  

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