[galaxy-dev] param name=type

2014-12-17 Thread Jorrit Boekel
Hi all, Just a heads-up, I had a tool.xml file in which a command line was called with a parameter called —type. I therefore set param name=“type” type=“select etc etc. to do: command —type $type Big mistake. This lead to errors as soon as the tool was modified in the workflow (set as

[galaxy-dev] disk space does not add up...

2014-12-17 Thread Langhorst, Brad
My glaaxy user data area is using 40T But the repots server only show usage of about 16T… Im nearly out of space and I’m not sure how to resolve the disparity. I have run the clearnup_datasets.py and other I’m running mainenance scripts like this: #!/bin/sh echo 'running galaxy maintenace

Re: [galaxy-dev] Functional tests using gzipped inputs have broken

2014-12-17 Thread John Chilton
Hey Peter, Thanks for the very detailed bug report - it really helped track things down. I have pushed a fix to next-stable and default (the bug never reached stable). https://bitbucket.org/galaxy/galaxy-central/commits/a74d32014b0512613042c2a44d0b946703a1fbcd The commit also includes a test

[galaxy-dev] Error when opening bowtie2 tool page

2014-12-17 Thread Anna Terry
Hi, I am getting an error page when I try to open the bowtie2 tool page (after selecting older version 0.2 a54de7e658f7 from drop down on version 0.3 c1ec08cb34f9 page). URL: http://../tool_runner/index File