Adding Custom Build is failing

Question: Adding Custom Build is failing

9 months ago by

mariawoer • 0 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 • 431 views

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modified 9 months ago • written 9 months ago by mariawoer • 0

9 months ago by

mariawoer • 0

mariawoer • 0 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 COMMENT • link modified 9 months ago • written 9 months ago by mariawoer • 0

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 REPLY • link written 8 months ago by Nate Coraor ♦ 3.2k

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 REPLY • link modified 8 weeks ago • written 8 weeks ago by mariawoer • 0

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