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
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 <jcsanchez2@gmail.com> 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/
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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 <p.j.a.cock@googlemail.com> 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 <jcsanchez2@gmail.com> 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/
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&redirect=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 <jcsanchez2@gmail.com> 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 <p.j.a.cock@googlemail.com> 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 <jcsanchez2@gmail.com> 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/
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 <jcsanchez2@gmail.com> 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&redirect=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 <jcsanchez2@gmail.com> 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 <p.j.a.cock@googlemail.com> 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 <jcsanchez2@gmail.com> 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/
participants (2)
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Juan Carlos -
Peter Cock