Pathway tools
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(Created page with "{{:template:mbn}} <div class="basic"> Be sure that /bin/csh is present. $ which csh /bin/csh Download install file (e.g., pathway-tools-16.0-linux-64-tier1-tier2-install) :It r...") |
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# Hostname of the machine on which Pathway Tools is running | # Hostname of the machine on which Pathway Tools is running | ||
# | # | ||
- | WWW-Server-Hostname localhost | + | <span style="color:red">WWW-Server-Hostname localhost</span> |
# Port number on which Pathway Tools should listen for WWW server | # Port number on which Pathway Tools should listen for WWW server |
Revision as of 12:55, 9 August 2012
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Be sure that /bin/csh is present.
$ which csh /bin/csh
Download install 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
6. Execute pathway-tools as web server mode
$ sudo pathway-tools -www
7. test
localhost:1555
8. Add Database
Tools → Browse PGDB registry → Select one for adding (e.g., Saccharophagus degradans) → click Fetch & install selected PGDBsDone!