Re: [galaxy-dev] Can existing SAM/BAM filter tools give me mapped/unmapped pairs?

2014-11-05 Thread Artem Tarasov
Hi Peter, I've uploaded updated tool_dependencies.xml to the Tool Shed, hopefully it works (I didn't bother installing Galaxy on local machine...) -- Artem On Tue, Nov 4, 2014 at 5:44 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm looking for a little advice on the

Re: [galaxy-dev] Unable to connect two tools in workflow editor

2014-11-05 Thread David Kelly
Thanks for the reply John. The problem was indeed with the datatype. The definition in datatypes_conf.xml was correct, but I was not importing it into registry.py. Once I made that change the workflow editor started working. Thanks! Regards, David On Sun, Nov 2, 2014 at 4:27 PM, John Chilton

Re: [galaxy-dev] Nothing being tested on Test and main Tool Shed?

2014-11-05 Thread Dave Bouvier
Peter, This was due to a number of issues with the testing framework, the last of which appears to have been resolved, and I see tools being tested in the framework log. I'll check again in the morning to see if any of the tools you listed below were still not tested. --Dave B. On

[galaxy-dev] Galaxy Not Displacing History

2014-11-05 Thread Jeremy Liu
Hi Galaxy Dev, I just pulled the latest updates for galaxy-dist with hg pull -u and then migrated over the postgres database with: sh manage_db.sh -c ./universe_wsgi.ini upgrade After restarting the server, my Galaxy instance would not show the history of datasets. The history was still there,

Re: [galaxy-dev] Galaxy Not Displacing History

2014-11-05 Thread Dannon Baker
This is usually an old cached version of the history panel interfering, or a javascript error that you'd see in the console. Can you clear browser cache, close out all Galaxy windows, and try again? If that still doesn't work, can you look in the javascript console to see if there are any errors?

[galaxy-dev] Integrating Docker-based tools within Galaxy failed

2014-11-05 Thread Weiyan Shen
Hi, I integrated Docker-based tools‍ SMALT whin my local Galaxy by the guid:https://github.com/apetkau/galaxy-hackathon-2014/tree/master/smalt, I found my Galaxy failed to integrate‍ with my docker. My docker images‍: = docker images REPOSITORY TAG IMAGE ID