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Old 06-30-2005, 12:11 PM   #1
Neruocomp
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Permissions Issues with Apache and InterProScan


Interproscan is a tool for scaning dna/protein sequence databases. It can be used through a web interface, which it provides itself. If you run the program without telling it you want to work it from the command line, it will spit out a whole bunch of html code, the web interface. When I run the configure script and tell it I want to use the web interface, it tells me to put this into httpd.conf

Alias /doc/ "/usr/local/share/iprscan/doc/html/"
Alias /images/ "/usr/local/share/iprscan/images/"
Alias /tmp/ "/usr/local/share/iprscan/tmp/"

ScriptAlias /iprscan/ "/usr/local/share/iprscan/bin/"

<Directory "/usr/local/share/iprscan/images">
Options Indexes MultiViews
AllowOverride None
Order allow,deny
Allow from all
</Directory>

<Directory "/usr/local/share/iprscan/tmp/">
Options FollowSymLinks Includes SymLinksIfOwnerMatch
IndexIgnore */.??* *~ *# */HEADER* */README* */RCS
AllowOverride AuthConfig Limit FileInfo

Order deny,allow
Deny from all
Allow from all
</Directory>

But when I try it http://localhost/iprscan/iprscan, it tells me it can't access it. Here is the output from the error log:

2:02:20 2005] [error] [client 127.0.0.1] (13)Permission denied: access to /iprscan/iprscan denied

I changed all the relevent directories to have apache as the group and group does have read/write access. Still it won't work.
ls -al /usr/local/share/iprscan/
drwxrwxrwx 3 root apache 4096 Jun 30 11:40 bin
drwxrwxr-x 4 root apache 4096 Jun 28 12:56 conf
-rwxr-xr-x 1 root root 37188 Apr 28 04:45 Config.pl
drwxr-xr-x 3 root apache 4096 Jun 29 10:00 data
drwxr-xr-x 5 root apache 4096 Jun 28 12:56 doc
-rw-r--r-- 1 root root 31084 Mar 29 03:53 FAQs.txt
drwxrwxr-x 5 root apache 4096 Jun 28 12:58 images
-rw-r--r-- 1 root root 63 Jun 30 11:11 .installed
drwxr-xr-x 7 root root 4096 Jun 28 12:58 lib
-rw-r--r-- 1 root root 47542 May 5 04:02 README.txt
-rw-r--r-- 1 root root 909 Jan 5 10:48 test.seq
drwxrwxr-x 4 root apache 4096 Jun 30 10:41 tmp

Running FC4 x86_64
Any ideas?
 
Old 07-04-2005, 12:10 PM   #2
Simon_6162
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Here are some of my thoughts, I hope one of them helps.

Sorry to ask the obvious but have you restarted apache since changing the http.conf file ?
/etc/init.d/httpd restart

Although not a final solution have you tried giving full access to everything to see if the problem lies there or somewhere else?
e.g.
chmod -R 777 /usr/local/share/iprscan

Also do you have selinux enabled? If you do then the problem could be coming form selinux permissions
 
Old 07-04-2005, 07:25 PM   #3
Neruocomp
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Yes, restarting httpd was one of the first things I did. And I also changed the permissions. But yea, selinux is running. Any ideas as how that is affecting it? Any ideas to get around it?
 
Old 07-05-2005, 05:23 AM   #4
Simon_6162
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Selinux is an extra set of permissions that I haven't really played about with yet. I suggest turning it off to see if it is this causeing the problem. Then we can sort out making it work with it on.

run system-config-securitylevel and disable selinux. You then have to reboot the machine.
 
Old 07-05-2005, 09:23 AM   #5
Neruocomp
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Thanks, that did it! As for getting it to work with Selinux, I have no idea how.
 
Old 07-05-2005, 09:53 AM   #6
Simon_6162
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Well done. At lest you can use your software now.

Here are the FC3 / apache notes regarding selinux.
http://fedora.redhat.com/docs/selinux-apache-fc3/

Regards

Simon
 
Old 07-05-2005, 12:30 PM   #7
Neruocomp
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I think I know what the problem is now. After I turned selinux back on, just to see if it would happen again. Well everything was still working. I think Selinux just needed to go and relabel the iprscan directory.
 
  


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