Re: [galaxy-dev] Internal Server Error when trying to install a tool from the Tool shed
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 <audreymannion@gmail.com> 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 <audreymannion@gmail.com> 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 <jmchilton@gmail.com> 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 <jmchilton@gmail.com> 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 <audreymannion@gmail.com> 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/
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 <jmchilton@gmail.com> 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
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
On Mon, Aug 18, 2014 at 11:56 AM, audrey michel <audreymannion@gmail.com> wrote: 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 <audreymannion@gmail.com
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 <jmchilton@gmail.com>
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 <jmchilton@gmail.com> 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 <audreymannion@gmail.com> 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/
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 <audreymannion@gmail.com> 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 <jmchilton@gmail.com> 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 <audreymannion@gmail.com> 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 < audreymannion@gmail.com> 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 <jmchilton@gmail.com>
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 <jmchilton@gmail.com> 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 <audreymannion@gmail.com> 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/
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 <audreymannion@gmail.com> 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 <audreymannion@gmail.com> 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 <jmchilton@gmail.com> 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
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 < audreymannion@gmail.com> 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 <jmchilton@gmail.com> 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
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 <jmchilton@gmail.com> 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 > <audreymannion@gmail.com> wrote: >> Hi, >> >> We get the following error when we try to install any tool from
On Mon, Aug 18, 2014 at 11:56 AM, audrey michel <audreymannion@gmail.com> wrote: the 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/
participants (2)
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audrey michel -
John Chilton