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No pathway Tools init file was found

asked 2017-08-29 09:48:59 -0500

mikeaalv gravatar image

Version 21.0 Linux red hat 6.8 Genome 2.28.2 After I install the pathway-tools, I find there is no ptools-init.dat file, which should exist as stated in the documents. If I open pathway-tools, there is warnings about no init file as well, though pathway-tools desktop mode still work. As I'd like to set a web sever, I need that file. Could you tell me how to fix that?

Another thing is about setting web mode. Do I need to set my install location and data&configure location as /usr/local/pathway-tools and /var for web usage? If that's not needed, while setting web mode, do I need root at any time?

Thanks a lot!


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answered 2017-08-29 21:32:25 -0500

Suzanne Paley gravatar image

The ptools-init.dat file should have been created during the installation process. You can recreate it by invoking pathway-tools with the -config command-line option, but I'm a little concerned that its absence might mean that something else went wrong during installation such that the process didn't complete. So I guess you can take your pick -- either re-run the installation, or run pathway-tools -config and see if either of those do the trick.

You can set your install location, etc. wherever you wish. The only reason I can think of to require root privileges is if you want to run your ptools web server on a privileged port, such as port 80.


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Thanks a lot. Actually, I have try install pathway-tools several times. No error or warning appear and there is no ptools-init.dat created. The system is linux redhat. I will try the configure one. Best. Yue Wu

mikeaalv gravatar imagemikeaalv ( 2017-08-29 22:17:14 -0500 )edit

Our guess is that you're running the install in sudo mode, and there is a mismatch regarding inheritance of user-specific environment variables and file write permissions. We recommend either just installing as yourself (in which case others won't be able to access it), or ...

Suzanne Paley gravatar imageSuzanne Paley ( 2017-08-30 16:14:03 -0500 )edit

... if you want to install in a central location, run the install from a shell where you have already logged in as root (and make sure all users have at least read access to all the generated paths).

Suzanne Paley gravatar imageSuzanne Paley ( 2017-08-30 16:18:36 -0500 )edit

When the installer runs, it creates a logfile /tmp/bitrock_installer_XXXX.log (XXXX=PID of the install process). If you're still having trouble and want us to look into it further, send that logfile to

Suzanne Paley gravatar imageSuzanne Paley ( 2017-08-30 16:19:38 -0500 )edit

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Asked: 2017-08-29 09:48:59 -0500

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Last updated: Aug 29 '17