From FreeBio

Contents 1 Installing Pathway tools 1.1 Install openmotif 2 Extra (for hacking): 2.1 Install Pathway tools source 2.2 Install ACL 8.1 2.3 Install Slime 3 How to add a pathway 4 Installing Pathway-genome databases 5 Installing perlcyc

Installing Pathway tools

• Go to http://biocyc.org/download.shtml
• Get the latest ptools installer
• Install the following files (if you are on Debian or Ubuntu)

       
        apt-get install csh emacs21 libmotif3 libmotif-dev xvfb xrgb
       

• Create a special file in /usr/local/bin/pathway-tools

#!/bin/bash

/usr/local/aic-export/pathway-tools/ptools/13.0/pathway-tools $*

• Open a terminal window, you must ssh -X localhost

        chmod 755 /usr/local/bin/pathway-tools

• Then, to get the navigator, execute pathway-tools at the command line.

        pathway-tools

• Navigator should come up.

Install openmotif

Instructions for getting Pathway tools to work with X

Extra (for hacking):

Install Pathway tools source

First request the source code: http://biocyc.org/download.shtml

• Because Pathway-tools has hardcoded its filenames to its source directories, you need to add the following hack:

                mkdir /homedir
                mkdir /homedir/brg
                ln -s /usr/local/aic-export /homedir/brg/aic

Install ACL 8.1

Download the appropriate binary from:

http://www.franz.com/ftp/pub/acl81express/

Find the file files.bu and copy it to your exe directory in pathway-tools.

For example, in Linux:

wget -c http://www.franz.com/ftp/pub/acl81express/linux86/acl81_express.bz2
tar xjvf acl81_express.bz2
cp acl81_express/files.bu /usr/local/pathway-tools/aic-export/pathway-tools/ptools/13.0/exe      

• Now you have all the libraries you need for slime.

Install Slime

To checkout from CVS you must first login to the repository: for bash

   export CVSROOT=:pserver:anonymous@common-lisp.net:/project/slime/cvsroot
   cvs login

or for csh:

   setenv CVSROOT :pserver:anonymous@common-lisp.net:/project/slime/cvsroot
   cvs login

Enter anonymous when prompted for the password. You can then check out the latest version with:

      cvs checkout slime

• Create a file called .swank.lisp in your home directory with the following line:

 (setq SWANK::*USE-DEDICATED-OUTPUT-STREAM* t)

• Edit your .emacs file with the following:

   (add-to-list 'load-path "~/src/slime/")  ; your SLIME directory
   (setq slime-lisp-implementations
         '((ptools ("/usr/local/bin/pathway-tools" "-lisp") :init slime-init-command)))
   (require 'slime)
   (slime-setup '(slime-repl))
   (setq slime-complete-symbol-function 'slime-fuzzy-complete-symbol)

Open an emacs buffer, and type:

 M-x slime

(this will automagically open pathway-tools lisp API) And this could be the beginning of a beautiful program!

How to add a pathway

(so 'meta)
(setq *metacyc* (current-kb))
(so 'med4)
(setq *med4* (current-kb))

(import-pathways '(pwy-5097) *metacyc* *med4* :overwrite? t :quiet? nil)
(save-kb)

(setq *cluster-orgs* 
    '(WH8102 SS120 PPAN PCORE NATL2A NATL1A MIT9515 MIT9313 MIT9312 MIT9303 MIT9301 MIT9211 MED4 CC9902 CC9605 AS9601))


(loop for org in *cluster-orgs*
   do (so org) 
   (import-pathways '(pwy-5097) *metacyc* (current-kb) :overwrite? t :quiet? nil)
   (save-kb))

Installing Pathway-genome databases

 cd ~/ptools-local/pgdbs/user
 tar xjvf user-13.0.tar.bz2
 

restart pathway-tools

Installing perlcyc

• Download the Perlcyc CPAN module to your home directory

 tar xzvf perlcyc_1.1.tar.gz
 cd perlcyc_1.1
 perl Makefile.PL
 make
 sudo make install

• Invoke the Pathway-tools external daemon:

 pathway-tools -api -lisp