snpEff: html report is not displaying after update
Hello Raj, This tool is from the Tool Shed and is maintained by the tool author. To contact them about functionality or problems, go to the Tool Shed at http://toolshed.g2.bx.psu.edu/, locate the repository (search by 'snpEff'), click on the name, in the the top far right corner locate the pull down menu "Repository Actions". Select "Contact repository owner" to send them a message. There have been many updates to Galaxy recently and it is possible that one of these had an impact on this tool. I am going to send your email to galaxy-dev@bx.psu.edu, to see if anyone else has had problems with this tool since the last distribution update. You may be asked to provide more information (be as specific as you can): the hg pull #, any customizations, python version, etc. Regards, Jen Galaxy team On 2/14/12 8:28 PM, Praveen Raj Somarajan wrote:
Hi All,
I updated galaxy recently to the latest version. Everything looks fine, except snpEff report html view. It was displaying properly (all tables and summary values) before the update, but the summary values are not displaying after the update. A sample screen-shot is attached for your reference. Could you please figure out this issue?
When I ran the same on command line, the reports were generated correctly. I assume, something (datatypes or preview) has changed by the update. Please let me know the work around on this?
Secondly, as we know, snpEff also generates a gene-wise annotation file along with other results, but somehow we cannot access this file through Galaxy. Though we see the link in the html report, but it seems the path is broken.
Let me know your suggestions.
Best,
Raj
------------------------------------------------------------------------ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system.
OCIMUMBIO SOLUTIONS (P) LTD
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Hi Raj, What's going on here is probably that the snpEff output is being sanitized by galaxy prior to display. The data is all intact, and I've recently added a config option 'sanitize_all_html' in changeset 6788:e58a87c91bc4 that will allow you to disable this for your local instance. If you update your local instance and set sanitize_all_html = False in your universe_wsgi.ini, you should see the expected output. -Dannon On Feb 22, 2012, at 3:36 PM, Jennifer Jackson wrote:
Hello Raj,
This tool is from the Tool Shed and is maintained by the tool author. To contact them about functionality or problems, go to the Tool Shed at http://toolshed.g2.bx.psu.edu/, locate the repository (search by 'snpEff'), click on the name, in the the top far right corner locate the pull down menu "Repository Actions". Select "Contact repository owner" to send them a message.
There have been many updates to Galaxy recently and it is possible that one of these had an impact on this tool. I am going to send your email to galaxy-dev@bx.psu.edu, to see if anyone else has had problems with this tool since the last distribution update.
You may be asked to provide more information (be as specific as you can): the hg pull #, any customizations, python version, etc.
Regards,
Jen Galaxy team
On 2/14/12 8:28 PM, Praveen Raj Somarajan wrote:
Hi All,
I updated galaxy recently to the latest version. Everything looks fine, except snpEff report html view. It was displaying properly (all tables and summary values) before the update, but the summary values are not displaying after the update. A sample screen-shot is attached for your reference. Could you please figure out this issue?
When I ran the same on command line, the reports were generated correctly. I assume, something (datatypes or preview) has changed by the update. Please let me know the work around on this?
Secondly, as we know, snpEff also generates a gene-wise annotation file along with other results, but somehow we cannot access this file through Galaxy. Though we see the link in the html report, but it seems the path is broken.
Let me know your suggestions.
Best,
Raj
------------------------------------------------------------------------ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system.
OCIMUMBIO SOLUTIONS (P) LTD
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
-
Dannon Baker -
Jennifer Jackson