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gbrowse + fcgi

Gregor Rot
Dear Gbrowse team,

i have a gbrowse2 up and running. The only problem is that i can't get
fcgi to work:

Apache error.log:
---
(104)Connection reset by peer: mod_fcgid: error reading data from
FastCGI server
Premature end of script headers: gbrowse
---

My gbrowse2.conf Apache fcgi part looks like this:

---
<IfModule mod_fcgid.c>
   Alias /fgb2 "/usr/lib/cgi-bin/gb2"
   <Location /fgb2>
     SetHandler   fcgid-script
   </Location>
   FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
   FcgidMinProcessesPerClass 1
   FcgidIOTimeout   600
   FcgidBusyTimeout 600
</IfModule>
---

I am using gbrowse version 2.48 on a Ubuntu 10.04.

Now, i would like to debug the problem but i don't know how. I can see
the cgi-bin executables in:

/usr/lib/cgi-bin/gb2

Any idea/help appreciated!

Kind regards,
Gregor

--
Gregor Rot
Bioinformatics Laboratory
Faculty of computer and information science
SI-1000 Ljubljana
Slovenia
http://www.fri.uni-lj.si/en/gregor-rot

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Fwd: gbrowse + fcgi

Gregor Rot
Hi all, can anybody help with the problem below?

Thanks,
Gregor

-------- Original Message --------
Subject: [Gmod-gbrowse] gbrowse + fcgi
Date: Fri, 13 Apr 2012 11:14:52 +0200
From: Gregor Rot <[hidden email]>
To: Gbrowse <[hidden email]>

Dear Gbrowse team,

i have a gbrowse2 up and running. The only problem is that i can't get
fcgi to work:

Apache error.log:
---
(104)Connection reset by peer: mod_fcgid: error reading data from
FastCGI server
Premature end of script headers: gbrowse
---

My gbrowse2.conf Apache fcgi part looks like this:

---
<IfModule mod_fcgid.c>
    Alias /fgb2 "/usr/lib/cgi-bin/gb2"
    <Location /fgb2>
      SetHandler   fcgid-script
    </Location>
    FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
    FcgidMinProcessesPerClass 1
    FcgidIOTimeout   600
    FcgidBusyTimeout 600
</IfModule>
---

I am using gbrowse version 2.48 on a Ubuntu 10.04.

Now, i would like to debug the problem but i don't know how. I can see
the cgi-bin executables in:

/usr/lib/cgi-bin/gb2

Any idea/help appreciated!

Kind regards,
Gregor

--
Gregor Rot
Bioinformatics Laboratory
Faculty of computer and information science
SI-1000 Ljubljana
Slovenia
http://www.fri.uni-lj.si/en/gregor-rot

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Re: Fwd: gbrowse + fcgi

Raymond Wan

Hi Gregor,


Quoting Gregor Rot <[hidden email]>:

> Apache error.log:
> ---
> (104)Connection reset by peer: mod_fcgid: error reading data from
> FastCGI server
> Premature end of script headers: gbrowse
> ---
>
> My gbrowse2.conf Apache fcgi part looks like this:
>
> ---
> <IfModule mod_fcgid.c>
>     Alias /fgb2 "/usr/lib/cgi-bin/gb2"
>     <Location /fgb2>
>       SetHandler   fcgid-script
>     </Location>
>     FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
>     FcgidMinProcessesPerClass 1
>     FcgidIOTimeout   600
>     FcgidBusyTimeout 600
> </IfModule>
> ---


I don't see anything wrong with the fcgi part in your Apache configuration.
When you access the server, is that the only error message you get in
error.log?  Most likely, you will get a set of error messages -- is that the
first one?

The other thing you want to look at is whether or not you have enabled that
module.  If so, should see it in /etc/apache2/mods-enabled/.  I don't know what
it was called in 10.04, but I guess it should be fcgid.{conf|load}.  if it isn't
there, you need to enable it with a2enmod.

If it is not there nor in mods-available, then you need to install it (of
course).

Something else you can try is to see if fastcgi works.  Perhaps trying it will
give you clues about what's wrong.  Before both, you should confirm that CGI
works.  I presume you already have?

Sorry, I can't think of anything else that could be wrong...

Ray




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Re: Fwd: gbrowse + fcgi

Gregor Rot
Hi Ray,

thank you, with you help (checking if mod_fcgi works) i found a perl
fastcgi test script by coincidence, and it was not working.

The solution was to install:

sudo apt-get install libfcgi-perl

on Ubuntu (so FCGI perl was missing). Now everything is working,

Thanks,
Gregor

On 4/19/2012 10:18 AM, Raymond Wan wrote:

>
> Hi Gregor,
>
>
> Quoting Gregor Rot<[hidden email]>:
>
>> Apache error.log:
>> ---
>> (104)Connection reset by peer: mod_fcgid: error reading data from
>> FastCGI server
>> Premature end of script headers: gbrowse
>> ---
>>
>> My gbrowse2.conf Apache fcgi part looks like this:
>>
>> ---
>> <IfModule mod_fcgid.c>
>>      Alias /fgb2 "/usr/lib/cgi-bin/gb2"
>>      <Location /fgb2>
>>        SetHandler   fcgid-script
>>      </Location>
>>      FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
>>      FcgidMinProcessesPerClass 1
>>      FcgidIOTimeout   600
>>      FcgidBusyTimeout 600
>> </IfModule>
>> ---
>
>
> I don't see anything wrong with the fcgi part in your Apache configuration.
> When you access the server, is that the only error message you get in
> error.log?  Most likely, you will get a set of error messages -- is that the
> first one?
>
> The other thing you want to look at is whether or not you have enabled that
> module.  If so, should see it in /etc/apache2/mods-enabled/.  I don't know what
> it was called in 10.04, but I guess it should be fcgid.{conf|load}.  if it isn't
> there, you need to enable it with a2enmod.
>
> If it is not there nor in mods-available, then you need to install it (of
> course).
>
> Something else you can try is to see if fastcgi works.  Perhaps trying it will
> give you clues about what's wrong.  Before both, you should confirm that CGI
> works.  I presume you already have?
>
> Sorry, I can't think of anything else that could be wrong...
>
> Ray
>
>
>
>
> -------------------------------------------------
> This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk
>

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