http://bioinformatics.ai.sri.com/ptools/installation-guide/released/
http://bioinformatics.ai.sri.com/ptools/installation-guide/released/unix.html#Linux%20install
need screen running and /usr/bin/Xvfb :55
where is screen? /usr/bin/screen
whay is SCREEN on toast?
Where is the start script for pathway on toast?
# pathway is installed in /usr/local
#
# these are the files inside /usr/local copied from toast
aic-export games lib64 pathway-tools_12.0 sbin
bin include libexec ptools-local share
etc lib pathway-tools ptools-local_12.0 src
# other directories important to pathways:
/usr/local/pathway-tools/aic-export
aic-init.lisp go mysql oracle pgdbs
aic-install htdocs old-metacyc-versions pathway-tools Readme.html
/usr/local/ptools-local
3485106364-3485106364-(none) ptools-init.dat~ ptools-survey-states
html ptools-init.dat.12 ptools-survey-states-
pgdbs ptools-init.dat.14 ptools-survey-states.old
ptools-init.dat ptools-init.dat.orig
script here:
/etc/init.d/pathway
/usr/local/aic-export/pathway-tools/ptools/14.0/
Build.dat graphs license misc pathway-tools.orig
doc help licenses patches
exe install logfiles pathway-tools
you need /usr/bin/Xvfb :55
and
/usr/bin/SCREEN
when installed run /usr/local/pathway-tools/pathway-tools
I received errors:
bash-3.2# ./pathway-tools
Warning: Loading sys:climxm.so failed with error:
libXp.so.6: cannot open shared object file: No such file or directory.
Warning: Loading sys:libScipAll.so failed with error:
/lib64/libc.so.6: version `GLIBC_2.7' not found (required by /usr/local/pathway-tools/aic-export/path
way-tools/ptools/15.0/exe/libScipAll.so).
;; Optimization settings: safety 1, space 1, speed 3, debug 1.
;; For a complete description of all compiler switches given the
;; current optimization settings evaluate (EXPLAIN-COMPILER-SETTINGS).
An unhandled error occurred during initialization:
Attempt to call
#("InitializeMyDrawingAreaQueryGeometry" 47237053447536 0 2
47237053447536 8)
for which the definition has not yet been (or is no longer) loaded.
added yum install xorg-x11-deprecated-libs !!! that worked perfectly####
Ran the /usr/local/pathway-tools/pathway-tools and a gui came up!
http://pathway-dev.stanford.edu
http://pathway.stanford.edu
to run the two different pathway applications, one is the desktop and one is the browser.
pathway has it's own browser so no apache necessary.
There was an error on the socket connection. the two programs could not talk.
We did a lot of trial and errors for this and found that all we had to do was
add the -lisp and the -api to the end of the startup command in /etc/init.d/pathway
and that worked!!!
there is no need in the 8 and above versions to start or run a server-socket.lisp for this. None whatsoever!
here is the test code to see if it is working:
perl -Mperlcyc -e '$c=perlcyc->new("yeast");@a=$c->all_pathways("")'
no errors then it works. it might fail and say connection error line 31.
Then that means the lisp and api are not running.
apache 26587 26586 0 Oct18 pts/0 00:00:17
/usr/local/pathway-tools/aic-export/pathway-tools/ptools/15.0//exe/pathway-tools-runtime
-- -exe-quiet -patch -go -www -no-blast -patch -org yeast -gene-link-db SGD
-lisp -api
this is how it looks with the -lisp and -api flags