Pathway-tools installation

From FreeBio


Contents

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Installing Pathway tools

  • Go to [1]
  • Select linux x32 Pathway tools with new user dbs: [2] 
        wget -c http://bioinformatics.ai.sri.com/ecocyc/dist/ptools-34987569/ptools-linux.tar.bz2
        apt-get install csh emacs21 libmotif3 libmotif-dev xvfb xrgb
        cd /usr/local
        tar xjvf ~/ptools-linux.tar.bz2
        cd /usr/local/aic-export/pathway-tools/ptools/10.5/install
        ./config-ptools
        <Enter your home directory>
  • Create a special file in /usr/local/bin/pathway-tools 
#!/bin/bash

/usr/local/aic-export/pathway-tools/ptools/10.5/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.
[edit]

Install openmotif

Instructions for getting Pathway tools to work with X

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Extra (for hacking):

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Install Pathway tools source 

             wget -c http://arep.med.harvard.edu/~zucker/ptools-src-10.5.tar.gz
             cd /usr/local
             tar xjvf ~/ptools-src-10.5.tar.gz
  • 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


[edit]

Install ACL 8.0 

       cd
       wget -c http://www.franz.com/ftp/pub/acl80express/linux86/acl80_express.bz2
       bunzip2 -c acl80_express.bz2 | tar xvf -
       cp -r /usr/local/aic-export/pathway-tools/ptools/10.5/exe/*  acl80_express
       mv /usr/local/aic-export/pathway-tools/ptools/10.5/exe /usr/local/aic-export/pathway-tools/ptools/10.5/exe.old
       mv acl80_express /usr/local/aic-export/pathway-tools/ptools/10.5/exe
  • Now you have all the libraries you need for slime.
[edit]

Install Slime

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

   export 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))
   ;;(setq inferior-lisp-program "/src/lsw/trunk/abcl") ; your Lisp system
   (require 'slime)
   (slime-setup)
   (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!

[edit]

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))
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Installing Pathway-genome databases 

 cd ~/ptools-local/pgdbs/user
 tar xjvf user-10.5.5.tar.bz2

restart pathway-tools

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Installing perlcyc 

 tar xzvf perlcyc_1.1.tar.gz
 cd perlcyc_1.1
 perl Makefile.PL
 make
 sudo make install
  • Check out example perlcyc code from gene.dfci.harvard.edu 
 export CVS_RSH=ssh
 cvs -d biocyc@gene.dfci.harvard.edu co BPHYS/perlcyc
 <ask me for password>
  • Invoke the Pathway-tools external daemon: 
 pathway-tools -api -lisp
  • Run the example percyc code in BPHYS/perlcyc
Retrieved from "http://bio.freelogy.org/wiki/Pathway-tools_installation"