On Wed, Jan 21, 2015 at 6:54 PM, John Chilton wrote:
> On Wed, Jan 21, 2015 at 10:35 AM, Wolfgang Maier
> 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,
ect: Re: [galaxy-dev] PATH set in tool env.sh leaking through to
> set_metadata.py
>
> 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.
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 to
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?
I need to think about how to solve this more generally bu
Yes, this is the local job runner on a single machine.
On 01/20/2015 06:52 PM, John Chilton 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)?
-John
On Tue, Jan 20, 2015 at 12:34 PM, Wol
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)?
-John
On Tue, Jan 20, 2015 at 12:34 PM, Wolfgang Maier
wrote:
> On 01/20/2015 06:20 PM, Wolfgang Maier wrote:
>>
>>
>> I have not seen this error
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 th
Hi,
I am not sure whether I am diagnosing this problem approximately right
or not, but it seems that with the latest release of Galaxy (stable
branch, latest_2015.01.13) enviroment variables set in a
tool-dependency's env.sh file and sourced before a job run are now
leaking through to
./scr
