Re: [scipion-users] Scipion3-install-3Dfsc

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Hi, you need to tell scipion how to activate conda.

I've got this in my config file (SCIPION_HOME/config/scipion.conf)

--------------------------scipin-conf -----------------------

[PLUGINS]
CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"

----------------------------------------------------------------

You will need to modify the path. Please note that this will not under 
tcsh/csh shells.

On 3/8/20 9:54, 范宏成 wrote:
> Hi all,
> When I installed the 3dfsc in scipion3 plugin 
> manager,(cenos7,anaconda3,cuda10.1) I faced some errors. See the 
> following:
> plugin.log
> 00001:   Found existing installation: scipion-em-fsc3d 3.0.5
> 00002:   Uninstalling scipion-em-fsc3d-3.0.5:
> 00003:     Successfully uninstalled scipion-em-fsc3d-3.0.5
> 00004:   Removing fsc3D-3.0 binaries...
> 00005:   Binary fsc3D-3.0 has been uninstalled successfully
> 00006:   Removing scipion-em-fsc3d plugin...
> 00007:   Processing 
> /home/fanhc/.cache/pip/wheels/d2/6a/3d/d8105cfbfb2f44c0c79b496cc6f3aa2f9bb2ae6a1a85790608/scipion_em_fsc3d-3.0.5-py3-none-any.whl
> 00008:   Requirement already satisfied: scipion-em in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> scipion-em-fsc3d==3.0.5) (3.0.0)
> 00009:   Requirement already satisfied: biopython==1.76 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> scipion-em->scipion-em-fsc3d==3.0.5) (1.76)
> 00010:   Requirement already satisfied: scipion-pyworkflow in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> scipion-em->scipion-em-fsc3d==3.0.5) (3.0.0a10)
> 00011:   Requirement already satisfied: numpy in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> biopython==1.76->scipion-em->scipion-em-fsc3d==3.0.5) (1.18.5)
> 00012:   Requirement already satisfied: bibtexparser in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (1.2.0)
> 00013:   Requirement already satisfied: pillow in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (7.1.2)
> 00014:   Requirement already satisfied: psutil in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (5.7.0)
> 00015:   Requirement already satisfied: requests in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (2.24.0)
> 00016:   Requirement already satisfied: configparser in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (5.0.0)
> 00017:   Requirement already satisfied: matplotlib in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (3.2.2)
> 00018:   Requirement already satisfied: future>=0.16.0 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> bibtexparser->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) 
> (0.18.2)
> 00019:   Requirement already satisfied: pyparsing>=2.0.3 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> bibtexparser->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) 
> (2.4.7)
> 00020:   Requirement already satisfied: idna<3,>=2.5 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (2.9)
> 00021:   Requirement already satisfied: chardet<4,>=3.0.2 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) (3.0.4)
> 00022:   Requirement already satisfied: certifi>=2017.4.17 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) 
> (2020.4.5.2)
> 00023:   Requirement already satisfied: 
> urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> requests->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) 
> (1.25.9)
> 00024:   Requirement already satisfied: kiwisolver>=1.0.1 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) 
> (1.2.0)
> 00025:   Requirement already satisfied: python-dateutil>=2.1 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) 
> (2.8.1)
> 00026:   Requirement already satisfied: cycler>=0.10 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) 
> (0.10.0)
> 00027:   Requirement already satisfied: six>=1.5 in 
> ./.scipion3env/lib/python3.6/site-packages (from 
> python-dateutil>=2.1->matplotlib->scipion-pyworkflow->scipion-em->scipion-em-fsc3d==3.0.5) 
> (1.15.0)
> 00028:   Installing collected packages: scipion-em-fsc3d
> 00029:   Successfully installed scipion-em-fsc3d-3.0.5
> 00030:   Collecting package metadata (repodata.json): ...working... 
> 00031:   done
> 00032:   Solving environment: ...working... 00033:   done
> 00034:   2020-08-03 03:48:21,120 INFO:  Error executing the operation: 
> install scipion-em-fsc3d
> 00035:   install scipion-em-fsc3d==3.0.5
> 00036:   Done (1.26 seconds)
> 00037:   WARNING!!: CONDA_ACTIVATION_CMD variable not defined. Relying 
> on conda being in the PATH
> 00038:   Building fsc3D-3.0 ...
> 00039:     Skipping command: wget -nv -c -O 
> /home/fanhc/scipion3/software/em/fsc3D-3.0.tgz.part 
> https://github.com/azazellochg/fsc3D/archive/3.0.tar.gz
> 00040:   mv -v /home/fanhc/scipion3/software/em/fsc3D-3.0.tgz.part 
> /home/fanhc/scipion3/software/em/fsc3D-3.0.tgz
> 00041:     All targets exist.
> 00042:   cd /home/fanhc/scipion3/software/em
> 00043:   tar -xf fsc3D-3.0.tgz
> 00044:   cd /home/fanhc/scipion3/software/em/fsc3D-3.0
> 00045:   conda env create -f environment.yml &&touch IS_INSTALLED
>
> plugin.er00001:   WARNING: You are using pip version 20.1.1; however, 
> version 20.2 is available.
> 00002:   You should consider upgrading via the 
> '/home/fanhc/scipion3/.scipion3env/bin/python -m pip install --upgrade 
> pip' command.
> 00003:   /bin/sh: line 1: 17742 Segmentation fault      (core dumped) 
> conda env create -f environment.yml
> 00004:   2020-08-03 03:48:21,120 ERROR:  Error executing the 
> operation: install scipion-em-fsc3d
>
> How to fix it? Thank you!
> Hongcheng Fan
>
>
>
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] Scipion3-install-3Dfsc

Image processing framework to integrate EM software packages.

Re: [scipion-users] Scipion3-install-3Dfsc