Question: Adding Custom Build is failing
0
gravatar for mariawoer
8 months ago by
mariawoer0
mariawoer0 wrote:

Hello all,

we are experiencing problems with adding custom builds in our local Galaxy. The data requirements (fasta format etc) are as specified under https://galaxyproject.org/learn/custom-genomes/ and we used NormalizeFasta with options to wrap sequence lines at 80 bases and to trim the title line at the first whitespace, just in case. However we always get: "Failed to convert Dataset" and no further information (see below). Unfortunately I can not find any clue to what is the problem in the log files.

enter image description here

Does anyone know what could be going wrong here? Any help would be much appreciated. Thanks!

Best

Maria

build genome galaxy custom • 403 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by mariawoer0
0
gravatar for Nate Coraor
8 months ago by
Nate Coraor3.2k
United States
Nate Coraor3.2k wrote:

Is this on usegalaxy.org? If so, could you send the email address or username you login with to galaxy-bugs@bx.psu.edu please?

ADD COMMENTlink written 8 months ago by Nate Coraor3.2k

This is on our local install of galaxy, not usegalaxy.org.

ADD REPLYlink modified 8 months ago • written 8 months ago by mariawoer0

Can you check your Galaxy logs for any errors that correlate with this failure?

ADD REPLYlink written 8 months ago by Nate Coraor3.2k
0
gravatar for mariawoer
8 months ago by
mariawoer0
mariawoer0 wrote:

Not really, I can't see any errors or warning messages (log level is set to DEBUG). Just a lot of messages similar to this:

[02/Mar/2018:01:00:03 +0200] "GET /api/histories/7ca8f1b7f24e5a2d/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "https://galaxy.palmuc.org/custom_builds" 
[02/Mar/2018:01:00:12 +0200] "PUT /api/users/df7a1f0c02a5b08e/custom_builds/test HTTP/1.1" 400 - "https://galaxy.palmuc.org/custom_builds"
ADD COMMENTlink modified 8 months ago • written 8 months ago by mariawoer0

Sorry, I missed your reply. Have you gotten this working? If not, can you explain a bit about how your Galaxy server is set up? Specifically:

  • What version of Galaxy?
  • Are you using a proxy server, and if so, which one, and how is it configured to proxy requests to Galaxy?
  • Are you using uWSGI or Paste as your application server for Galaxy?
ADD REPLYlink written 7 months ago by Nate Coraor3.2k

In return I unfortunately missed your reply, I'm just now getting back to the issue.

What version of Galaxy?

We upgraded to v18.05 recently but this did not solve the issue.

Are you using uWSGI or Paste as your application server for Galaxy?

We are still using paste but plan to switch to uWSGI in the near future.

Are you using a proxy server, and if so, which one, and how is it configured to proxy requests to Galaxy?

Yes, a standard Apache/Proxy setup. This is our apache2/vhosts.d/galaxy.palmuc.org.conf file:

<VirtualHost *:80>

    ServerAdmin pal.admin@lrz.uni-muenchen.de
    ServerName galaxy.palmuc.org
    RewriteEngine On
    RewriteRule (.*) https://galaxy.palmuc.org$1 [R=301,L]
</VirtualHost>

<IfDefine SSL>
   <IfModule ssl_module>
      <VirtualHost *:443>
        ServerAdmin pal.admin@lrz.uni-muenchen.de
        ServerName galaxy.palmuc.org
        #Include /etc/apache2/vhosts.d/503php.include

        #<Location />
        #Require ip 141.84.51.170
        #Require ip 62.216.203.55
        #</Location>

        RewriteEngine on
        RewriteRule ^(.*) http://localhost:8080$1 [P]
        RewriteRule ^/static/style/(.*) /opt/galaxy/static/june_2007_style/blue/$1 [L]
        RewriteRule ^/static/scripts/(.*) /opt/galaxy/static/scripts/packed/$1 [L]
        RewriteRule ^/static/(.*) /opt/galaxy/static/$1 [L]
        RewriteRule ^/favicon.ico /opt/galaxy/static/favicon.ico [L]
        RewriteRule ^/robots.txt /opt/galaxy/static/robots.txt [L]

        <Location "/">
        RequestHeader set X-URL-SCHEME https
        # Compress all uncompressed content.
        SetOutputFilter DEFLATE
        SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
        SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
        SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary
        </Location>

        <Location "/static">
        # Allow browsers to cache everything from /static for 6 hours
        ExpiresActive On
        ExpiresDefault "access plus 6 hours"
        </Location>

        SSLEngine on
        SSLCertificateFile /etc/galaxy/sec/ssl/certs/palmuc.org.crt
        SSLCertificateKeyFile /etc/galaxy/sec/ssl/private/palmuc.org.key
        SSLCertificateChainFile /etc/galaxy/sec/ssl/certs/Intermediate_CA_Bundle.crt
        SSLOptions StrictRequire
        SSLProtocol all -SSLv2 -SSLv3

      </VirtualHost>
    </IfModule>
</IfDefine>
ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by mariawoer0
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