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tbepler / topaz

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.
GNU General Public License v3.0
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topaz insttaltion issue #73

Closed diffracteD closed 3 years ago

diffracteD commented 3 years ago

Hi, I'm trying to use topaz for very first time. But I'm stuck with an installation issue.

[abhisek@c101030 topaz-master]$ conda create -n topaz python=2.7
awk: fatal: cannot open file `/programs/x86_64-linux/system/bin/conda__evcouplings' for reading (No such file or directory)
grep: /programs/x86_64-linux/sphire/sphire.rc: No such file or directory
Fetching package metadata .........
Solving package specifications: .

Package plan for installation in environment /home/abhisek/.conda/envs/topaz:

The following NEW packages will be INSTALLED:

    certifi:    2016.2.28-py27_0
    openssl:    1.0.2l-0        
    pip:        9.0.1-py27_1    
    python:     2.7.13-0        
    readline:   6.2-2           
    setuptools: 36.4.0-py27_1   
    sqlite:     3.13.0-0        
    tk:         8.5.18-0        
    wheel:      0.29.0-py27_0   
    zlib:       1.2.11-0        

Proceed ([y]/n)? y

#
# To activate this environment, use:
# > source activate topaz
#
# To deactivate this environment, use:
# > source deactivate topaz
#

[abhisek@c101030 topaz-master]$ source activate topaz
basename: invalid option -- 'b'
Try 'basename --help' for more information.
dirname: invalid option -- 'b'
Try 'dirname --help' for more information.
-bash: /programs/x86_64-linux/gromacs/2020.1_cu9.2.88/gromacs_extlib/gromacs-2020.1-ptxb/share/man: syntax error: operand expected (error token is "/programs/x86_64-linux/gromacs/2020.1_cu9.2.88/gromacs_extlib/gromacs-2020.1-ptxb/share/man")

Can you please help me out to recover this error? It's really unclear to me, what caused this error. Thanks Abhisek

tbepler commented 3 years ago

This looks like a problem with your system or possibly your conda install, not with topaz. I recommend contacting your system administrator, if you have one, about this problem. As a side note, I highly recommend using python 3 rather than 2.

diffracteD commented 3 years ago

I tried using > pip3 install topaz-em It worked as it seems. Final message was:

Requirement already satisfied: torch>=1.0.0 in /usr/local/lib/python3.7/site-packages (from topaz-em) (1.4.0)
Installing collected packages: topaz-em
Successfully installed topaz-em-0.2.4
tbepler commented 3 years ago

Great! Closing this issue since it seems to be resolved and not topaz related.