Pathway tools

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 PGDBs