Hi Wolfgang,
That's probably because you have those extra labels in some of the files
in your directory now. If you use the extra options, it is now necessary
to set that COUNT.
HTH,
S
On 08/02/2018 01:35 PM, Lugmayr, Wolfgang wrote:
> Hi Sjors,
>
> thanks for the quick fix.
>
> It is working now after the git pull as before if you set:
> export RELION_QSUB_EXTRA_COUNT=2
>
> Otherwise the following error message appears:
> $ relion
> WARNING: cannot find qsub_extra1 in the defined joboptions!
> zsh: segmentation fault relion
>
> Cheers,
> Wolfgang
>
>
>
> ----- Original Message -----
> From: "Sjors Scheres" <[log in to unmask]>
> To: "Mailinglist CCPEM" <[log in to unmask]>
> Sent: Thursday, 2 August, 2018 12:14:05
> Subject: Re: [ccpem] relion3 beta extra1 & extra2 environment variables?
>
> And I have changed the default behaviour to the one from before, so that
> you do not need to change anything if you just want to use 2 extra
> variables.
>
> Just use git pull and recompile to make the changes effective.
>
> HTH,
>
> Sjors
>
>
>
> On 08/02/2018 10:38 AM, Lugmayr, Wolfgang wrote:
>> Hi,
>>
>> we are using the RELION_QSUB_EXTRA1 and RELION_QSUB_EXTRA2 environment variables to change the GUI and substitute values in the submission script.
>>
>> In the current git version this does not seem to work anymore.
>>
>> When i search the code its still somewhere there:
>> ./src/pipeline_jobs.cpp: if (joboptions.find("qsub_extra2") != joboptions.end())
>> ./src/pipeline_jobs.cpp: replacing["XXXextra2XXX"] = joboptions["qsub_extra2"].getString();
>> ./src/pipeline_jobs.cpp:If these options are not enough for your standard jobs, you may define two extra variables: XXXextra1XXX and XXXextra2XXX \
>> ./src/pipeline_jobs.cpp:Their help text is set by the environment variables RELION_QSUB_EXTRA1 and RELION_QSUB_EXTRA2 \
>> ./src/pipeline_jobs.cpp:Likewise, default values for the extra entries can be set through environment variables RELION_QSUB_EXTRA1_DEFAULT and RELION_QSUB_EXTRA2_DEFAULT. \
>>
>> this feature was quite useful. is it still available?
>>
>> cheers,
>> Wolfgang
>>
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>>
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--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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