Re: [galaxy-dev] blast2html

[Juan Carlos]

HI,
well in case anyone come across a similar problem. I finally found out that
it wasnt a blast specific issue but a general thing. This is I could not
visualize any data, even the one i uploaded, but this didnt happen and
could see everything if i had the module x_accel_redirect disable.
After a while found that this issue was easily solve just adding a "listen
80;" under the nginx configuration.
Now it looks something like this:
server {
client_max_body_size 10G;
listen   80;
server_name  localhost;

#charset koi8-r;

#access_log  logs/host.access.log  main;

...


Didnt check how to solve this issue with the equivalent Apache2 xsendfile.
Just wonder if this should be added to the
https://wiki.galaxyproject.org/Admin/Config/nginxProxy page.


Regards
jc














On Tue, Oct 13, 2015 at 3:01 PM, Juan Carlos  wrote:

>
>
> Hi all,
> doing some more test realized that when leave "sanitize_all_html = False"
> i cant actually see any html result. So really thinking is something to do
> with the apache2 settings.
> I followed all the step at
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy?action=show=Admin%2FConfig%2FApache+Proxy
> but maybe didnt take into account something else.
> Anyone has any idea to help?
>
> thanks!
> jc
>
>
>
>
> On Fri, Oct 9, 2015 at 12:24 PM, Juan Carlos  wrote:
>
>> Hi Peter,
>>
>> Just checked it and the HTML output from BLAST+ seems ok.
>> As you said I also think is related to some issue with the security of
>> Galaxy. Everywhere i checked they only mention the sanitize parameter, dont
>> know what else could be, even thinking if it could be something in the
>> apache2 configuration
>> so still trying to find out
>>
>> thanks
>>
>> On Thu, Oct 8, 2015 at 7:04 PM, Peter Cock 
>> wrote:
>>
>>> Hi Juan,
>>>
>>> It does sounds like something in Galaxy's HTML security
>>> code could be to blame...
>>>
>>> Do you have any other HTML producing tools installed?
>>> It would be useful to see how their output behaves. e.g.
>>> The BLAST+ tools offer (very simple ugly) HTML output
>>> directly.
>>>
>>> Peter
>>>
>>> On Thu, Oct 8, 2015 at 7:54 AM, Juan Carlos 
>>> wrote:
>>> >
>>> > Hi,
>>> >
>>> > I'm new to galaxy and trying to set up a local blast tool, and maybe
>>> this is
>>> > due to a silly mistake
>>> > So far so good all is working but when trying to use blast2html i just
>>> get a
>>> > "blank" page (even if the html is being generated), this happens when
>>> using
>>> > the recommended setting in the configuration file
>>> > "sanitize_all_html = False"
>>> >
>>> > Tried with "sanitize_all_html = True" and was able to see the results
>>> but
>>> > with the message of the results being stripped.to be sure that at
>>> least
>>> > was working
>>> >
>>> > Thanks for any help!!
>>> > jc
>>> >
>>> > ___
>>> > 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:
>>> >   https://lists.galaxyproject.org/
>>> >
>>> > To search Galaxy mailing lists use the unified search at:
>>> >   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
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[galaxy-dev] blast2html

[Juan Carlos]

Hi,

I'm new to galaxy and trying to set up a local blast tool, and maybe this
is due to a silly mistake
So far so good all is working but when trying to use blast2html i just get
a "blank" page (even if the html is being generated), this happens when
using the recommended setting in the configuration file
"sanitize_all_html = False"

Tried with "sanitize_all_html = True" and was able to see the results but
with the message of the results being stripped.to be sure that at least
was working

Thanks for any help!!
jc
___
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Re: [galaxy-dev] blast2html

[Peter Cock]

Hi Juan,

It does sounds like something in Galaxy's HTML security
code could be to blame...

Do you have any other HTML producing tools installed?
It would be useful to see how their output behaves. e.g.
The BLAST+ tools offer (very simple ugly) HTML output
directly.

Peter

On Thu, Oct 8, 2015 at 7:54 AM, Juan Carlos  wrote:
>
> Hi,
>
> I'm new to galaxy and trying to set up a local blast tool, and maybe this is
> due to a silly mistake
> So far so good all is working but when trying to use blast2html i just get a
> "blank" page (even if the html is being generated), this happens when using
> the recommended setting in the configuration file
> "sanitize_all_html = False"
>
> Tried with "sanitize_all_html = True" and was able to see the results but
> with the message of the results being stripped.to be sure that at least
> was working
>
> Thanks for any help!!
> jc
>
> ___
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___
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Re: [galaxy-dev] blast2html

[Juan Carlos]

Hi Peter,

Just checked it and the HTML output from BLAST+ seems ok.
As you said I also think is related to some issue with the security of
Galaxy. Everywhere i checked they only mention the sanitize parameter, dont
know what else could be, even thinking if it could be something in the
apache2 configuration
so still trying to find out

thanks

On Thu, Oct 8, 2015 at 7:04 PM, Peter Cock 
wrote:

> Hi Juan,
>
> It does sounds like something in Galaxy's HTML security
> code could be to blame...
>
> Do you have any other HTML producing tools installed?
> It would be useful to see how their output behaves. e.g.
> The BLAST+ tools offer (very simple ugly) HTML output
> directly.
>
> Peter
>
> On Thu, Oct 8, 2015 at 7:54 AM, Juan Carlos  wrote:
> >
> > Hi,
> >
> > I'm new to galaxy and trying to set up a local blast tool, and maybe
> this is
> > due to a silly mistake
> > So far so good all is working but when trying to use blast2html i just
> get a
> > "blank" page (even if the html is being generated), this happens when
> using
> > the recommended setting in the configuration file
> > "sanitize_all_html = False"
> >
> > Tried with "sanitize_all_html = True" and was able to see the results but
> > with the message of the results being stripped.to be sure that at
> least
> > was working
> >
> > Thanks for any help!!
> > jc
> >
> > ___
> > 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:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>
___
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