On Wed, Jan 21, 2015 at 6:54 PM, John Chilton email@example.com wrote:
On Wed, Jan 21, 2015 at 10:35 AM, Wolfgang Maier firstname.lastname@example.org wrote:
On 21.01.2015 16:11, John Chilton wrote:
So the tool dependency stuff didn't change - but the local job runner now behaves like the other job runners (DRMAA, PBS, etc...) so you have uncovered a bug for all of them I think. Is this a tool shed tool or a locally created dependency?
This is a tool shed tool (package_mimodd_0_1_5), but one I uploaded myself (I discovered the bug when I did a test install after updating our local Galaxy).
I need to think about how to solve this more generally but if you want a quick work around - I think it would work to just replace "python" in $GALAXY_ROOT/set_metadata.sh with a hard-coded path to Galaxy's python or perhaps just "python2".
Since I can change the tool shed tool a more "global" solution could be to simply remove the "python" symlink from the python3 virtualenv after its created and have the tool use "python3" explicitly at runtime. I'll try whether that works, but I think it should.
This sounds like a better short-term solution to me - this way older versions of Galaxy will still be able to use the recipe. I created a Trello issue to track the longer term fix of isolating metadata generation from the tool environment - which is needed but could be a little disruptive so I would rather push it off until after the next release.
Opps - I forgot the link and forgot to cc the mailing list.
Sorry for the inconvenience and thanks for bringing this to our attention.
No problem. I'm glad if I could help with something instead of just asking questions all the time.
On Tue, Jan 20, 2015 at 12:52 PM, John Chilton email@example.com wrote:
Are you using the local job runner (this will be the case if you haven't explicitly configured something like pbs or DRMAA in your job_conf.xml file)?
On Tue, Jan 20, 2015 at 12:34 PM, Wolfgang Maier firstname.lastname@example.org wrote:
On 01/20/2015 06:20 PM, Wolfgang Maier wrote:
I have not seen this error before (I believe not with latest_2014.10.06)
update: confirmed this now. It's enough to hg update to latest_2014.10.06 and things are working again.
The difference is that when building the dependency shell command the latest release seems to put the call to set_metadata.sh into that command, while before it seems it was run separately.