Re: [galaxy-dev] wrapper for tool with multiple outputs

2017-01-04 Thread Devon Ryan
Hi Jochen, Don't have it use /tmp, but rather the current working directory and then everything will work. Galaxy jobs are run in individual working directories, so you can exploit that to ensure that files aren't overwritten. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data

[galaxy-dev] wrapper for tool with multiple outputs

2017-01-04 Thread Jochen Bick
Hi, I have a tool that produces multiple output files a log file, two bam files. (https://github.com/nugentechnologies/nudup) The tool it self provides an option called --out to specify a path to a directory with a prefix that will be added to the output files: --out /tmp/out this will

[galaxy-dev] installation error on venv dependencies.xml

2017-01-04 Thread Bakker, Linda
Hi All, I posted my question before the holidays but i got not reply. Can someone please point me in the right direction? I am having some problems with my tool dependencies to setup a python venv. Dependencies.xml looks like this: [X] [X][cid:7b48a44d-07dd-4838-8f90-5024d9d22593] When i