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t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
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error in SLAMdunk: ".local/lib/python2.7/site-packages/slamdunk/contrib/ngm: No such file or directory" #55

Closed amitblum closed 5 years ago

amitblum commented 5 years ago

Hello I tried to install SLAMdunk using your recommendation: conda create --name myenv -c bioconda slamdunk

From some reasons, while runnig SLAMdunk I have error. The log file message is: .local/lib/python2.7/site-packages/slamdunk/contrib/ngm: No such file or directory

ls for this directory, give me the following: build-ngm.sh build-rnaseqreadsimulator.sh build-samtools.sh build-varscan.sh init.py init.pyc nextgenmap

Anything that I should do in order to solve that problem?

Thanks Amit

t-neumann commented 5 years ago

Hm what is in your conda env folder?

Must be something like this:

~/.conda/envs/myenv/lib/python2.7/site-packages/slamdunk/contrib/ngm

Does this exist?

If yes, try this before loading the conda env:

export PYTHONNOUSERSITE=1

amitblum commented 5 years ago

thanks. will try it

t-neumann commented 5 years ago

@amitblum can this be closed?