Dear Ruben and Carlos Oscar,
thank you very much! I'll try and report but I am afraid that it
will take some time.....
bw Dieter
------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: [log in to unmask]
------------------------------------------------------------------------
Am 16.12.2018 um 22:15 schrieb Carlos Oscar S. Sorzano:
> Dear Dieter,
>
> DeepConsensus has been integrated into Scipion but it has not been
> included in the scipion current release yet. At some moment in the
> near future, the release of the packages will be different from the
> release of Scipion. The different packages will be plugins and you
> will be notified when new plugins or newer versions are available.
>
> At the moment, in order to use it you, have to switch to co_tensor_new
> development branch. I am afraid that it cannot be executed in command
> line.
> If you want to install scipion version with DeepConsensus integrated,
> you just need to use the following commands ( It will be almost
> automatic once the release will include DeepConsensus).
>
>
> WARNING, in order to use GPU acceleration you will need CUDA-8.0 and
> CUDNN-6
> or CUDA-9.0 and CUDNN-7 (https://developer.nvidia.com/cudnn).
> Basically, to install CUDNN you just have to uncompress and copy to
> CUDA path subfolds lib64 and lib the contained fields
>
> #Install scipion and xmipp to try deepConsensus before release
>
> Suppose we want to install scipion in /home/ruben/app/scipion and
> xmipp in /home/ruben/app/xmipp_bundle
>
> #First install xmipp
>
> cd /home/ruben/app/
> mkdir xmipp_bundle
> cd xmipp_bundle
>
> wget https://raw.githubusercontent.com/I2PC/xmipp/devel/xmipp -O xmipp
> chmod a+x xmipp
> ./xmipp all N=8 br=co_tensor_new
> #Edit xmipp.conf. to use CUDA e.g. with gedit or nano
> nano xmipp.conf
> CUDA=True
>
> #Then, install scipion
> cd /home/ruben/app/
> git clone https://github.com/I2PC/scipion
> cd scipion
> git checkout co_tensor_new_new
> ./scipion config
> #Edit ./config/scipion.conf. to use CUDA e.g. with gedit or nano
> nano config.scipion.conf
> CUDA_LIB = /home/ruben/app/cudas/cuda-8-CDNN_6/lib64
> CUDA_BIN = /home/ruben/app/cudas/cuda-8-CDNN_6/bin
> NVCC_INCLUDE = /home/ruben/app/cudas/cuda-8-CDNN_6/include
> CUDA=True
>
> #Tell scipion where xmipp is
> ./scipion installp -p
> /home/ruben/app/xmipp_bundle/src/scipion-em-xmipp --devel --noBin
> ln -s /home/ruben/app/xmipp_bundle/src/scipion-em-xmipp/xmipp3
> /home/ruben/app/scipion/software/lib/python2.7/site-packages/
> #Edit ~/.config/scipion/scipion.conf to tell where xmipp binaries are
> nano -w ~/.config/scipion/scipion.conf
> XMIPP_HOME = /home/ruben/app/xmipp_bundle/build
>
> #Finally, install deepConsensus
> ./scipion installb deepLearnigToolkit
>
>
> Now you can create scipion project by
>
> ./scipion
>
> The GUI will be launched
>
> In order to use deepConsensus, import the micrographs, the particles,
> possibly pick with another picker
> and fill the protocol form for deepConsensus.
> To find it easily you can use ctrl+f
> and type DeepConsensus
>
> If you have any further problem, please do not hesitate to tell us.
>
> Kind regards, Ruben and Carlos Oscar
>
> El 16/12/2018 a las 8:26, Dieter Blaas escribió:
>> Dear Carlos and all,
>>
>> I was wondering how to use DeepConsensus for the elimination of
>> already picked 'bad' virus particles instead of cleaning the data set
>> (in relion) with multiple Class3D runs and cutting off
>> _rlnLogLikeliContribution outlayers. Since the paper on Deep
>> Consensus states that the program had been integrated into Scipion I
>> upgraded my installation following the description
>> (https://github.com/I2PC/scipion/wiki/How-to-Install). However, it
>> still reports "version-1.1.beta". Even after a completely new install
>> the version did not change. Can anybody please indicate whether it is
>> possible to run DeepConsensus on a relion star file and if so how?
>> I'd very much like to use it in the old-fashioned way from command
>> line :-).
>>
>> Thanks, bw Dieter
>>
>> ------------------------------------------------------------------------
>> Dieter Blaas,
>> Max F. Perutz Laboratories
>> Medical University of Vienna
>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>> Dr. Bohr Gasse 9/3,
>> A-1030 Vienna, Austria,
>> Tel: 0043 1 4277 61630,
>> Fax: 0043 1 4277 9616,
>> e-mail: [log in to unmask]
>> ------------------------------------------------------------------------
>>
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