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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--
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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