Internal Server Error when trying to install a tool from the Tool shed

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Internal Server Error when trying to install a tool from the Tool shed

audrey michel
Hi,

We get the following error when we try to install any tool from the Tool shed when using the Admin panel:


Internal Server Error

Galaxy was unable to successfully complete your request

An error occurred.

This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.

The error has been logged to our team.





We would be grateful if you could advise on this issue.

Kind Regards,
Audrey Michel
Baranov Lab
School of Biochemistry & Cell Biology
University College Cork
Ireland



___________________________________________________________
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Re: Internal Server Error when trying to install a tool from the Tool shed

John Chilton-4
I am not sure what the problem is - more details would really help.
For instance - What version of Galaxy are you using? What repository
are you trying to install? Do other repositories work? Does the Galaxy
log have a more complete stack trace?

Any additional details would be most helpful.

Thanks,
-John

On Tue, Aug 12, 2014 at 9:11 AM, audrey michel <[hidden email]> wrote:

> Hi,
>
> We get the following error when we try to install any tool from the Tool
> shed when using the Admin panel:
>
>
> Internal Server Error
>
> Galaxy was unable to successfully complete your request
>
> An error occurred.
>
> This may be an intermittent problem due to load or other unpredictable
> factors, reloading the page may address the problem.
>
> The error has been logged to our team.
>
>
>
>
>
> We would be grateful if you could advise on this issue.
>
> Kind Regards,
> Audrey Michel
> Baranov Lab
> School of Biochemistry & Cell Biology
> University College Cork
> Ireland
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Internal Server Error when trying to install a tool from the Tool shed

John Chilton-4
Okay - I am replying in thread but I not to your original message
because there might be private stuff in the log you sent me. It looks
like you were trying to install fastqdump from the main tool shed. So
I setup a fresh Galaxy instance this morning and the only two things I
changed in the universe_wsgi.ini file were admin_users and
tool_dependency_dir (required to install tool dependencies) and this
install worked for me. Your error message had "Bad Status Line" in it
- so it sounds like you were getting non-sense back from the tool
shed.

This could be because there is some proxy interfering with this
request, it could be that it was just an intermittent problem with the
tool shed, or ... some configuration problem potentially? I am not
sure.

It looks like you had cloned galaxy-dist directly - I think it is
better to stay on a particular branch - I would do this:

hg pull
hg update latest_2014.08.11

To make sure you have the latest and greatest Galaxy and then retry?

If you still have problems and it is the same strack trace - please
let me know. Next up would be to eliminate the proxy theory - not sure
how to do that though :(.

-John

On Wed, Aug 13, 2014 at 4:36 PM, John Chilton <[hidden email]> wrote:

> I am not sure what the problem is - more details would really help.
> For instance - What version of Galaxy are you using? What repository
> are you trying to install? Do other repositories work? Does the Galaxy
> log have a more complete stack trace?
>
> Any additional details would be most helpful.
>
> Thanks,
> -John
>
> On Tue, Aug 12, 2014 at 9:11 AM, audrey michel <[hidden email]> wrote:
>> Hi,
>>
>> We get the following error when we try to install any tool from the Tool
>> shed when using the Admin panel:
>>
>>
>> Internal Server Error
>>
>> Galaxy was unable to successfully complete your request
>>
>> An error occurred.
>>
>> This may be an intermittent problem due to load or other unpredictable
>> factors, reloading the page may address the problem.
>>
>> The error has been logged to our team.
>>
>>
>>
>>
>>
>> We would be grateful if you could advise on this issue.
>>
>> Kind Regards,
>> Audrey Michel
>> Baranov Lab
>> School of Biochemistry & Cell Biology
>> University College Cork
>> Ireland
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Internal Server Error when trying to install a tool from the Tool shed

John Chilton-4
Hello Audrey,

  Please keep responses on list - it ensures people smarter than me
can respond :). Can you tell me what is sitting in front of Galaxy -
Apache, Nginx, uwsgi, etc... and send the configurations if possible?
I believe the out-of-the-box uwsgi configuration has some problems
with really long URL query strings which using the tool shed does
produce.

-John


On Mon, Aug 18, 2014 at 11:56 AM, audrey michel <[hidden email]> wrote:

> Hi John,
>
> We tried the following on another server where there is no proxy, and we are
> able to install tools from this new instance:
>
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist/
>
>
>  $ hg clone https://bitbucket.org/galaxy/galaxy-dist/
> destination directory: galaxy-dist
> requesting all changes
> adding changesets
> adding manifests
> adding file changes
> added 14316 changesets with 48369 changes to 8546 files (+1 heads)
> updating to branch default
> 3597 files updated, 0 files merged, 0 files removed, 0 files unresolved
>
> We then modified just the admin_users, tool_dependency_dir, port and
> localhost. This was sufficient to allow us to use the toolshed to install
> tools on this particular instance of galaxy.
>
> So it would appear to be a proxy issue with our other instance of galaxy
> which is behind a proxy. Could you advise us on where we need to add
> http_proxy as we don't know which file(s) to add this to? We already set the
> filter-with = proxy-prefix in the universe_wsgi.ini fiel.
>
> Thanks in advance,
> Audrey
>
>
>
>
>
>
>
>
> On Mon, Aug 18, 2014 at 11:31 AM, audrey michel <[hidden email]>
> wrote:
>>
>> Hi John,
>>
>> Thanks for the suggestions. We are going to try a new install on one of
>> our other servers and see if the problem occurs there or not.
>>
>> Will update you when we do this.
>>
>> Thanks.
>> Audrey
>>
>>
>> On Fri, Aug 15, 2014 at 8:20 PM, John Chilton <[hidden email]> wrote:
>>>
>>> Okay - I am replying in thread but I not to your original message
>>> because there might be private stuff in the log you sent me. It looks
>>> like you were trying to install fastqdump from the main tool shed. So
>>> I setup a fresh Galaxy instance this morning and the only two things I
>>> changed in the universe_wsgi.ini file were admin_users and
>>> tool_dependency_dir (required to install tool dependencies) and this
>>> install worked for me. Your error message had "Bad Status Line" in it
>>> - so it sounds like you were getting non-sense back from the tool
>>> shed.
>>>
>>> This could be because there is some proxy interfering with this
>>> request, it could be that it was just an intermittent problem with the
>>> tool shed, or ... some configuration problem potentially? I am not
>>> sure.
>>>
>>> It looks like you had cloned galaxy-dist directly - I think it is
>>> better to stay on a particular branch - I would do this:
>>>
>>> hg pull
>>> hg update latest_2014.08.11
>>>
>>> To make sure you have the latest and greatest Galaxy and then retry?
>>>
>>> If you still have problems and it is the same strack trace - please
>>> let me know. Next up would be to eliminate the proxy theory - not sure
>>> how to do that though :(.
>>>
>>> -John
>>>
>>> On Wed, Aug 13, 2014 at 4:36 PM, John Chilton <[hidden email]>
>>> wrote:
>>> > I am not sure what the problem is - more details would really help.
>>> > For instance - What version of Galaxy are you using? What repository
>>> > are you trying to install? Do other repositories work? Does the Galaxy
>>> > log have a more complete stack trace?
>>> >
>>> > Any additional details would be most helpful.
>>> >
>>> > Thanks,
>>> > -John
>>> >
>>> > On Tue, Aug 12, 2014 at 9:11 AM, audrey michel
>>> > <[hidden email]> wrote:
>>> >> Hi,
>>> >>
>>> >> We get the following error when we try to install any tool from the
>>> >> Tool
>>> >> shed when using the Admin panel:
>>> >>
>>> >>
>>> >> Internal Server Error
>>> >>
>>> >> Galaxy was unable to successfully complete your request
>>> >>
>>> >> An error occurred.
>>> >>
>>> >> This may be an intermittent problem due to load or other unpredictable
>>> >> factors, reloading the page may address the problem.
>>> >>
>>> >> The error has been logged to our team.
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> We would be grateful if you could advise on this issue.
>>> >>
>>> >> Kind Regards,
>>> >> Audrey Michel
>>> >> Baranov Lab
>>> >> School of Biochemistry & Cell Biology
>>> >> University College Cork
>>> >> Ireland
>>> >>
>>> >>
>>> >>
>>> >> ___________________________________________________________
>>> >> Please keep all replies on the list by using "reply all"
>>> >> in your mail client.  To manage your subscriptions to this
>>> >> and other Galaxy lists, please use the interface at:
>>> >>   http://lists.bx.psu.edu/
>>> >>
>>> >> To search Galaxy mailing lists use the unified search at:
>>> >>   http://galaxyproject.org/search/mailinglists/
>>
>>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Internal Server Error when trying to install a tool from the Tool shed

audrey michel
Hi John,

We are using Apache with the following configuration:

#Configuration file for galaxy
<VirtualHost *:80>
        #ServerName localhost:80
        ServerName X.X.X:80  #I have commented out our serverName for the purpose of this email
DocumentRoot /mnt/workspace/DATA/galaxy
RewriteEngine on
#RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/static/style/(.*) /galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*) /galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
        <Directory /mnt/workspace/DATA/galaxy>
         #      Options +Includes
               #Order allow,deny
Order deny,allow
Deny from All
                Allow from X.X.X  #I have commented out our subnet for the purpose of this email
               #Allow from All
        </Directory>
</Virtualhost>

Thanks in advance for any suggestions,
Audrey


On Tue, Aug 19, 2014 at 8:53 PM, John Chilton <[hidden email]> wrote:
Hello Audrey,

  Please keep responses on list - it ensures people smarter than me
can respond :). Can you tell me what is sitting in front of Galaxy -
Apache, Nginx, uwsgi, etc... and send the configurations if possible?
I believe the out-of-the-box uwsgi configuration has some problems
with really long URL query strings which using the tool shed does
produce.

-John


On Mon, Aug 18, 2014 at 11:56 AM, audrey michel <[hidden email]> wrote:
> Hi John,
>
> We tried the following on another server where there is no proxy, and we are
> able to install tools from this new instance:
>
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist/
>
>
>  $ hg clone https://bitbucket.org/galaxy/galaxy-dist/
> destination directory: galaxy-dist
> requesting all changes
> adding changesets
> adding manifests
> adding file changes
> added 14316 changesets with 48369 changes to 8546 files (+1 heads)
> updating to branch default
> 3597 files updated, 0 files merged, 0 files removed, 0 files unresolved
>
> We then modified just the admin_users, tool_dependency_dir, port and
> localhost. This was sufficient to allow us to use the toolshed to install
> tools on this particular instance of galaxy.
>
> So it would appear to be a proxy issue with our other instance of galaxy
> which is behind a proxy. Could you advise us on where we need to add
> http_proxy as we don't know which file(s) to add this to? We already set the
> filter-with = proxy-prefix in the universe_wsgi.ini fiel.
>
> Thanks in advance,
> Audrey
>
>
>
>
>
>
>
>
> On Mon, Aug 18, 2014 at 11:31 AM, audrey michel <[hidden email]>
> wrote:
>>
>> Hi John,
>>
>> Thanks for the suggestions. We are going to try a new install on one of
>> our other servers and see if the problem occurs there or not.
>>
>> Will update you when we do this.
>>
>> Thanks.
>> Audrey
>>
>>
>> On Fri, Aug 15, 2014 at 8:20 PM, John Chilton <[hidden email]> wrote:
>>>
>>> Okay - I am replying in thread but I not to your original message
>>> because there might be private stuff in the log you sent me. It looks
>>> like you were trying to install fastqdump from the main tool shed. So
>>> I setup a fresh Galaxy instance this morning and the only two things I
>>> changed in the universe_wsgi.ini file were admin_users and
>>> tool_dependency_dir (required to install tool dependencies) and this
>>> install worked for me. Your error message had "Bad Status Line" in it
>>> - so it sounds like you were getting non-sense back from the tool
>>> shed.
>>>
>>> This could be because there is some proxy interfering with this
>>> request, it could be that it was just an intermittent problem with the
>>> tool shed, or ... some configuration problem potentially? I am not
>>> sure.
>>>
>>> It looks like you had cloned galaxy-dist directly - I think it is
>>> better to stay on a particular branch - I would do this:
>>>
>>> hg pull
>>> hg update latest_2014.08.11
>>>
>>> To make sure you have the latest and greatest Galaxy and then retry?
>>>
>>> If you still have problems and it is the same strack trace - please
>>> let me know. Next up would be to eliminate the proxy theory - not sure
>>> how to do that though :(.
>>>
>>> -John
>>>
>>> On Wed, Aug 13, 2014 at 4:36 PM, John Chilton <[hidden email]>
>>> wrote:
>>> > I am not sure what the problem is - more details would really help.
>>> > For instance - What version of Galaxy are you using? What repository
>>> > are you trying to install? Do other repositories work? Does the Galaxy
>>> > log have a more complete stack trace?
>>> >
>>> > Any additional details would be most helpful.
>>> >
>>> > Thanks,
>>> > -John
>>> >
>>> > On Tue, Aug 12, 2014 at 9:11 AM, audrey michel
>>> > <[hidden email]> wrote:
>>> >> Hi,
>>> >>
>>> >> We get the following error when we try to install any tool from the
>>> >> Tool
>>> >> shed when using the Admin panel:
>>> >>
>>> >>
>>> >> Internal Server Error
>>> >>
>>> >> Galaxy was unable to successfully complete your request
>>> >>
>>> >> An error occurred.
>>> >>
>>> >> This may be an intermittent problem due to load or other unpredictable
>>> >> factors, reloading the page may address the problem.
>>> >>
>>> >> The error has been logged to our team.
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> We would be grateful if you could advise on this issue.
>>> >>
>>> >> Kind Regards,
>>> >> Audrey Michel
>>> >> Baranov Lab
>>> >> School of Biochemistry & Cell Biology
>>> >> University College Cork
>>> >> Ireland
>>> >>
>>> >>
>>> >>
>>> >> ___________________________________________________________
>>> >> Please keep all replies on the list by using "reply all"
>>> >> in your mail client.  To manage your subscriptions to this
>>> >> and other Galaxy lists, please use the interface at:
>>> >>   http://lists.bx.psu.edu/
>>> >>
>>> >> To search Galaxy mailing lists use the unified search at:
>>> >>   http://galaxyproject.org/search/mailinglists/
>>
>>
>


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Internal Server Error when trying to install a tool from the Tool shed

audrey michel
Hi John,

We also tried adding the proxy server ip address as follows to some hgrc files (but this did not resolve the issue):


1. Added the following to the hgrc file in /etc/mercurial/hgrc – :

[http_proxy]

host = X.X.X.X:8080  #ip address of our proxy server


2. Also added the above two lines to the hgrc file in /galaxy/galaxy-dist/.hg)


3. We also created a .hgrc file in /home/galaxy/ with just the following two lines:

[http_proxy]

host = X.X.X.X:8080 #ip address of our proxy server

but none of the above resolved the toolshed download problem.


Maybe there are locations where we need to add the proxy server address?


Regards,

Audrey



On Wed, Aug 20, 2014 at 5:05 PM, audrey michel <[hidden email]> wrote:
Hi John,

We are using Apache with the following configuration:

#Configuration file for galaxy
<VirtualHost *:80>
        #ServerName localhost:80
        ServerName X.X.X:80  #I have commented out our serverName for the purpose of this email
DocumentRoot /mnt/workspace/DATA/galaxy
RewriteEngine on
#RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/static/style/(.*) /galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*) /galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
        <Directory /mnt/workspace/DATA/galaxy>
         #      Options +Includes
               #Order allow,deny
Order deny,allow
Deny from All
                Allow from X.X.X  #I have commented out our subnet for the purpose of this email
               #Allow from All
        </Directory>
</Virtualhost>

Thanks in advance for any suggestions,
Audrey


On Tue, Aug 19, 2014 at 8:53 PM, John Chilton <[hidden email]> wrote:
Hello Audrey,

  Please keep responses on list - it ensures people smarter than me
can respond :). Can you tell me what is sitting in front of Galaxy -
Apache, Nginx, uwsgi, etc... and send the configurations if possible?
I believe the out-of-the-box uwsgi configuration has some problems
with really long URL query strings which using the tool shed does
produce.

-John


On Mon, Aug 18, 2014 at 11:56 AM, audrey michel <[hidden email]> wrote:
> Hi John,
>
> We tried the following on another server where there is no proxy, and we are
> able to install tools from this new instance:
>
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist/
>
>
>  $ hg clone https://bitbucket.org/galaxy/galaxy-dist/
> destination directory: galaxy-dist
> requesting all changes
> adding changesets
> adding manifests
> adding file changes
> added 14316 changesets with 48369 changes to 8546 files (+1 heads)
> updating to branch default
> 3597 files updated, 0 files merged, 0 files removed, 0 files unresolved
>
> We then modified just the admin_users, tool_dependency_dir, port and
> localhost. This was sufficient to allow us to use the toolshed to install
> tools on this particular instance of galaxy.
>
> So it would appear to be a proxy issue with our other instance of galaxy
> which is behind a proxy. Could you advise us on where we need to add
> http_proxy as we don't know which file(s) to add this to? We already set the
> filter-with = proxy-prefix in the universe_wsgi.ini fiel.
>
> Thanks in advance,
> Audrey
>
>
>
>
>
>
>
>
> On Mon, Aug 18, 2014 at 11:31 AM, audrey michel <[hidden email]>
> wrote:
>>
>> Hi John,
>>
>> Thanks for the suggestions. We are going to try a new install on one of
>> our other servers and see if the problem occurs there or not.
>>
>> Will update you when we do this.
>>
>> Thanks.
>> Audrey
>>
>>
>> On Fri, Aug 15, 2014 at 8:20 PM, John Chilton <[hidden email]> wrote:
>>>
>>> Okay - I am replying in thread but I not to your original message
>>> because there might be private stuff in the log you sent me. It looks
>>> like you were trying to install fastqdump from the main tool shed. So
>>> I setup a fresh Galaxy instance this morning and the only two things I
>>> changed in the universe_wsgi.ini file were admin_users and
>>> tool_dependency_dir (required to install tool dependencies) and this
>>> install worked for me. Your error message had "Bad Status Line" in it
>>> - so it sounds like you were getting non-sense back from the tool
>>> shed.
>>>
>>> This could be because there is some proxy interfering with this
>>> request, it could be that it was just an intermittent problem with the
>>> tool shed, or ... some configuration problem potentially? I am not
>>> sure.
>>>
>>> It looks like you had cloned galaxy-dist directly - I think it is
>>> better to stay on a particular branch - I would do this:
>>>
>>> hg pull
>>> hg update latest_2014.08.11
>>>
>>> To make sure you have the latest and greatest Galaxy and then retry?
>>>
>>> If you still have problems and it is the same strack trace - please
>>> let me know. Next up would be to eliminate the proxy theory - not sure
>>> how to do that though :(.
>>>
>>> -John
>>>
>>> On Wed, Aug 13, 2014 at 4:36 PM, John Chilton <[hidden email]>
>>> wrote:
>>> > I am not sure what the problem is - more details would really help.
>>> > For instance - What version of Galaxy are you using? What repository
>>> > are you trying to install? Do other repositories work? Does the Galaxy
>>> > log have a more complete stack trace?
>>> >
>>> > Any additional details would be most helpful.
>>> >
>>> > Thanks,
>>> > -John
>>> >
>>> > On Tue, Aug 12, 2014 at 9:11 AM, audrey michel
>>> > <[hidden email]> wrote:
>>> >> Hi,
>>> >>
>>> >> We get the following error when we try to install any tool from the
>>> >> Tool
>>> >> shed when using the Admin panel:
>>> >>
>>> >>
>>> >> Internal Server Error
>>> >>
>>> >> Galaxy was unable to successfully complete your request
>>> >>
>>> >> An error occurred.
>>> >>
>>> >> This may be an intermittent problem due to load or other unpredictable
>>> >> factors, reloading the page may address the problem.
>>> >>
>>> >> The error has been logged to our team.
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> We would be grateful if you could advise on this issue.
>>> >>
>>> >> Kind Regards,
>>> >> Audrey Michel
>>> >> Baranov Lab
>>> >> School of Biochemistry & Cell Biology
>>> >> University College Cork
>>> >> Ireland
>>> >>
>>> >>
>>> >>
>>> >> ___________________________________________________________
>>> >> Please keep all replies on the list by using "reply all"
>>> >> in your mail client.  To manage your subscriptions to this
>>> >> and other Galaxy lists, please use the interface at:
>>> >>   http://lists.bx.psu.edu/
>>> >>
>>> >> To search Galaxy mailing lists use the unified search at:
>>> >>   http://galaxyproject.org/search/mailinglists/
>>
>>
>



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Internal Server Error when trying to install a tool from the Tool shed

audrey michel
Hi John,

We resolved the toolshed download issue by adding an entry for https_proxy in our /etc/environment file. 

Thanks for all your help.
Audrey


On Wed, Aug 20, 2014 at 5:55 PM, audrey michel <[hidden email]> wrote:
Hi John,

We also tried adding the proxy server ip address as follows to some hgrc files (but this did not resolve the issue):


1. Added the following to the hgrc file in /etc/mercurial/hgrc – :

[http_proxy]

host = X.X.X.X:8080  #ip address of our proxy server


2. Also added the above two lines to the hgrc file in /galaxy/galaxy-dist/.hg)


3. We also created a .hgrc file in /home/galaxy/ with just the following two lines:

[http_proxy]

host = X.X.X.X:8080 #ip address of our proxy server

but none of the above resolved the toolshed download problem.


Maybe there are locations where we need to add the proxy server address?


Regards,

Audrey



On Wed, Aug 20, 2014 at 5:05 PM, audrey michel <[hidden email]> wrote:
Hi John,

We are using Apache with the following configuration:

#Configuration file for galaxy
<VirtualHost *:80>
        #ServerName localhost:80
        ServerName X.X.X:80  #I have commented out our serverName for the purpose of this email
DocumentRoot /mnt/workspace/DATA/galaxy
RewriteEngine on
#RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/static/style/(.*) /galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*) /galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
        <Directory /mnt/workspace/DATA/galaxy>
         #      Options +Includes
               #Order allow,deny
Order deny,allow
Deny from All
                Allow from X.X.X  #I have commented out our subnet for the purpose of this email
               #Allow from All
        </Directory>
</Virtualhost>

Thanks in advance for any suggestions,
Audrey


On Tue, Aug 19, 2014 at 8:53 PM, John Chilton <[hidden email]> wrote:
Hello Audrey,

  Please keep responses on list - it ensures people smarter than me
can respond :). Can you tell me what is sitting in front of Galaxy -
Apache, Nginx, uwsgi, etc... and send the configurations if possible?
I believe the out-of-the-box uwsgi configuration has some problems
with really long URL query strings which using the tool shed does
produce.

-John


On Mon, Aug 18, 2014 at 11:56 AM, audrey michel <[hidden email]> wrote:
> Hi John,
>
> We tried the following on another server where there is no proxy, and we are
> able to install tools from this new instance:
>
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist/
>
>
>  $ hg clone https://bitbucket.org/galaxy/galaxy-dist/
> destination directory: galaxy-dist
> requesting all changes
> adding changesets
> adding manifests
> adding file changes
> added 14316 changesets with 48369 changes to 8546 files (+1 heads)
> updating to branch default
> 3597 files updated, 0 files merged, 0 files removed, 0 files unresolved
>
> We then modified just the admin_users, tool_dependency_dir, port and
> localhost. This was sufficient to allow us to use the toolshed to install
> tools on this particular instance of galaxy.
>
> So it would appear to be a proxy issue with our other instance of galaxy
> which is behind a proxy. Could you advise us on where we need to add
> http_proxy as we don't know which file(s) to add this to? We already set the
> filter-with = proxy-prefix in the universe_wsgi.ini fiel.
>
> Thanks in advance,
> Audrey
>
>
>
>
>
>
>
>
> On Mon, Aug 18, 2014 at 11:31 AM, audrey michel <[hidden email]>
> wrote:
>>
>> Hi John,
>>
>> Thanks for the suggestions. We are going to try a new install on one of
>> our other servers and see if the problem occurs there or not.
>>
>> Will update you when we do this.
>>
>> Thanks.
>> Audrey
>>
>>
>> On Fri, Aug 15, 2014 at 8:20 PM, John Chilton <[hidden email]> wrote:
>>>
>>> Okay - I am replying in thread but I not to your original message
>>> because there might be private stuff in the log you sent me. It looks
>>> like you were trying to install fastqdump from the main tool shed. So
>>> I setup a fresh Galaxy instance this morning and the only two things I
>>> changed in the universe_wsgi.ini file were admin_users and
>>> tool_dependency_dir (required to install tool dependencies) and this
>>> install worked for me. Your error message had "Bad Status Line" in it
>>> - so it sounds like you were getting non-sense back from the tool
>>> shed.
>>>
>>> This could be because there is some proxy interfering with this
>>> request, it could be that it was just an intermittent problem with the
>>> tool shed, or ... some configuration problem potentially? I am not
>>> sure.
>>>
>>> It looks like you had cloned galaxy-dist directly - I think it is
>>> better to stay on a particular branch - I would do this:
>>>
>>> hg pull
>>> hg update latest_2014.08.11
>>>
>>> To make sure you have the latest and greatest Galaxy and then retry?
>>>
>>> If you still have problems and it is the same strack trace - please
>>> let me know. Next up would be to eliminate the proxy theory - not sure
>>> how to do that though :(.
>>>
>>> -John
>>>
>>> On Wed, Aug 13, 2014 at 4:36 PM, John Chilton <[hidden email]>
>>> wrote:
>>> > I am not sure what the problem is - more details would really help.
>>> > For instance - What version of Galaxy are you using? What repository
>>> > are you trying to install? Do other repositories work? Does the Galaxy
>>> > log have a more complete stack trace?
>>> >
>>> > Any additional details would be most helpful.
>>> >
>>> > Thanks,
>>> > -John
>>> >
>>> > On Tue, Aug 12, 2014 at 9:11 AM, audrey michel
>>> > <[hidden email]> wrote:
>>> >> Hi,
>>> >>
>>> >> We get the following error when we try to install any tool from the
>>> >> Tool
>>> >> shed when using the Admin panel:
>>> >>
>>> >>
>>> >> Internal Server Error
>>> >>
>>> >> Galaxy was unable to successfully complete your request
>>> >>
>>> >> An error occurred.
>>> >>
>>> >> This may be an intermittent problem due to load or other unpredictable
>>> >> factors, reloading the page may address the problem.
>>> >>
>>> >> The error has been logged to our team.
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>
>>> >> We would be grateful if you could advise on this issue.
>>> >>
>>> >> Kind Regards,
>>> >> Audrey Michel
>>> >> Baranov Lab
>>> >> School of Biochemistry & Cell Biology
>>> >> University College Cork
>>> >> Ireland
>>> >>
>>> >>
>>> >>
>>> >> ___________________________________________________________
>>> >> Please keep all replies on the list by using "reply all"
>>> >> in your mail client.  To manage your subscriptions to this
>>> >> and other Galaxy lists, please use the interface at:
>>> >>   http://lists.bx.psu.edu/
>>> >>
>>> >> To search Galaxy mailing lists use the unified search at:
>>> >>   http://galaxyproject.org/search/mailinglists/
>>
>>
>




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