Failing to install VEP dependencies
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2.4 years ago

I'm trying to install VEP, but am getting stuck installing its dependencies.

I try to install as suggested here https://www.ensembl.org/info/docs/tools/vep/script/index.html

cd ~/bin
git clone https://github.com/Ensembl/ensembl-vep.git
cd ensembl-vep
perl INSTALL.pl

But I get this error:

ERROR: DBI module not found. VEP requires the DBI perl module to function

http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements

So, I then try and install DBI as suggested here https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements

cpanm DBI

But I get this error:

Can't write to cpanm home '/Users/michaelflower/.cpanm': You should fix it with chown/chmod first.

How to I 'fix' it with chown/chmod??

yep cpanm DBI • 2.5k views
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When you can always use conda to install.

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I’ve tried installing in conda, it fails. It keeps failing to resolve a conflict

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Make sure you set the channel order correctly. Do the following. Then it should work.

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
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I'm trying that, but not looking promising. It's still having the same problem ...

michaelflower@Michaels-MacBook-Pro-2 ~/bin/ensembl-vep
$ conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top

michaelflower@Michaels-MacBook-Pro-2 ~/bin/ensembl-vep
$ conda config --add channels bioconda
Warning: 'bioconda' already in 'channels' list, moving to the top
conda config --add channels conda-forge

michaelflower@Michaels-MacBook-Pro-2 ~/bin/ensembl-vep
$ conda config --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top

michaelflower@Michaels-MacBook-Pro-2 ~/bin/ensembl-vep
$ conda install -c bioconda ensembl-vep
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: | ^[- 
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