Pathway tools
From CSBLwiki
(Difference between revisions)
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localhost:1555 | localhost:1555 | ||
+ | ;Another story | ||
Tools → Flux Balance Analysis : Add Database (It can be only used in desktop mode) | Tools → Flux Balance Analysis : Add Database (It can be only used in desktop mode) | ||
Tools → Browse PGDB registry → Select one for adding (e.g., Saccharophagus | Tools → Browse PGDB registry → Select one for adding (e.g., Saccharophagus |
Revision as of 13:00, 9 August 2012
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Be sure that /bin/csh is present.
$ which csh
/bin/csh
Download installation file (e.g., pathway-tools-16.0-linux-64-tier1-tier2-install) It requires license.
Install
$ sudo ./pathway-tools-16.0-linux-64-tier1-tier2-install)
Make pathway-tools accessible in any directory
$ sudo rm -f /usr/local/bin/pathway-tools $ sudo cp /usr/local/pathway-tools/pathway-tools /usr/local/bin/pathway-tools $ chmod 755 /usr/local/bin/pathway-tools
YOU HAVE TO EXECUTE PATHWAY-TOOLS WITH SUPER USER
Edit /home/ptools-local/ptools-init.dat
Remove # from this file. (purple mark)
######################################################################## # Parameters for Pathway Tools when running in WWW server mode # -- Setting these parameters is MANDATORY if you run Pathway Tools in # WWW server mode. # Hostname of the machine on which Pathway Tools is running # WWW-Server-Hostname localhost # Port number on which Pathway Tools should listen for WWW server # requests, and which Pathway Tools will insert in URLs within the # WWW pages that it generates. The standard port for WWW servers is 80, # but this may require root privileges for starting up Pathway Tools. # WWW-Server-Port 1555 # The root directories of files (e.g., .html, .shtml, .js) served by # the server. You can specify one directory or a list of directories # separated by a '+' (no spaces). If a list, the directories will # be searched in the order given when serving static files. Do not # include a trailing slash or backslash at the end of the directories. # WWW-Html-Root-Dir /usr/local/pathway-tools/aic-export/htdocs # Set this to "Y" (no quotes) if you would like gzip to apply compression on # CSS, HTML and JavaScript files served by the web server. # This will generate gzip compressed files in the same # directories as the original files, therefore enough # disk space and write access must be provided for these # directories to set this parameter to "Y". # The PATH variable must also have a path to gzip for this to work. # The default value for this parameter is "N". # The value "Y" is applicable only to non Microsoft Windows systems. # WWW-Use-Gzip N # Set this to "N" (no quotes) to disable the use of SVG to draw compounds and reactions. # SVG (Scalable Vector Graphics) is a web standard for drawing figures. # As of 16.0, Pathway Tools will use SVG on browsers that support it. # This parameter can turn off SVG, in which case the older style of graphics # will be used. # WWW-Use-SVG Y # Set this to "Y" (no quotes) to enable the web group feature. # The default value for this parameter is "N". # If web accounts database is set up, groups will be stored in the database # otherwise they will be stored in ptools-local/groups. NOTE: the first time # groups are turned on with a database, the schema will be upgraded, so PLEASE # make sure you make a backup first! # WWW-Enable-Groups N # Set this to "all" (no quotes) or a list of organism IDs, separated # by one or several '+' if several organism IDs, if you would like the # title of page objects to be the "Cyc" name of the database and not # the organism name. # If "all" is specified, it will apply to all databases. If a list of # organism IDs is given, it will only apply to these organisms. # The default value is "none". # Use-Cyc-Name none
Execute pathway-tools as web server mode
$ sudo pathway-tools -www
test
localhost:1555
- Another story
Tools → Flux Balance Analysis : Add Database (It can be only used in desktop mode)
Tools → Browse PGDB registry → Select one for adding (e.g., Saccharophagus degradans) → click Fetch & install selected PGDBsDone!