search

Bioconductor / ensemblVEP

[DEPRECATED] R Interface to Ensembl Variant Effect Predictor
https://bioconductor.org/packages/ensemblVEP
5 stars 4 forks source link

VEPFlags error #3

Closed audyavar closed 5 years ago

audyavar commented 5 years ago

I installed the latest version of VEP from Github and ensembleVEP from Bioconductor with version 95 of the annotation cache on Centos OS. When I am running the steps from the ensemblVEP R tutorial, I get the following errors. Please advise.

library(ensemblVEP) param <- VEPFlags() Error in validObject(.Object) : invalid class “VEPFlags” object: Ensembl >=88 requires vep script (not variant_effect_predictor.pl) param <- VEPFlags(flags=list(host="useastdb.ensembl.org"), version=94) Error in validObject(.Object) : invalid class “VEPFlags” object: Ensembl >=88 requires vep script (not variant_effect_predictor.pl)

lshep commented 5 years ago

Can you please display the results of running the following command line:

which vep
vep --help
audyavar commented 5 years ago

I fixed the issue. It seems that running ensemblVEP in R needs VEP path added to default bashrc profile.

Best

Akshata

From: lshep notifications@github.com Sent: Thursday, April 11, 2019 7:45 AM To: Bioconductor/ensemblVEP Cc: Akshata Udyavar; Author Subject: Re: [Bioconductor/ensemblVEP] VEPFlags error (#3)

Can you please display the results of running the following command line:

which vep vep --help

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/ensemblVEP/issues/3#issuecomment-482144924, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ACQU0dx_ynafE_SswkHDnhxEbzR4l89Iks5vf0qbgaJpZM4cRyoP.

lshep commented 5 years ago

excellent - I was actually just typing that suggestion too!

HeikoBre commented 3 years ago

I am running into the same problem - however, I have no idea how too add the VEP path to my default bashrc profile? Could you help me set this up?

lshep commented 3 years ago

@HeikoBre what operating system are you using?

HeikoBre commented 3 years ago

Dear @lshep I am running Mac OS Mojave Version 10.14.6 on a MacBook Pro. Thank you for your help!

LiNk-NY commented 3 years ago

Hi @HeikoBre, You should be able to add it to your ~/.bash_profile on Mac via something like: 

echo "$HOME/bin/vep" >> ~/.bash_profile

Where the path points to your vep installation.

The installation instructions here may be of some help: https://uswest.ensembl.org/info/docs/tools/vep/script/vep_download.html#macos

HeikoBre commented 3 years ago

Hi @LiNk-NY ,

If I run the command in terminal it adds the line

/Users/admin/ensembl-vep/

to my .bash_profile file. Unfortunately, it doesn't change the error I encounter in R... I tried to relaunch R, didn't change anything though...

LiNk-NY commented 3 years ago

@HeikoBre Make sure you are pointing to the vep installation / script and not the folder. The ending of your path has to look like the vep you would use to run a command (see example below where ./vep is used)

# Example of VEP command line:
./vep --cache --offline --format vcf --vcf --force_overwrite \
--dir_cache /opt/vep/.vep/ \
--dir_plugins /opt/vep/.vep/Plugins/ \
--input_file /opt/vep/.vep/input/my_input.vcf \
--output_file /opt/vep/.vep/output/my_output.vcf \
--custom /opt/vep/.vep/custom/my_extra_data.bed,BED_DATA,bed,exact,1 \
--plugin dbNSFP,/opt/vep/.vep/Plugins/dbNSFP.gz,ALL

Make sure to log out and log back in to apply changes to your ~/.bash_profile.

HeikoBre commented 3 years ago

Thanks, I tried to go through the installation steps again to make sure I didn't have any upstream problems. When using cpanm DBD::mysql I encounter a problem. My logfile says "Can't link/include C library 'ssl', 'crypto', aborting." Probably I need to fix this first... However, I couldn't find a quick solution for it...

hpages commented 3 years ago

@HeikoBre Maybe this helps. This document is a step-by-step record of what we install on our Mac builders.

Then take a look at the next section (4.11 Install Ensembl VEP script) for the installation of the Ensembl VEP script itself.

Hope this helps.

HeikoBre commented 3 years ago

Dear @hpages

Thank you for your suggestion! I struggle to append /usr/local/opt/mysql-client/bin to PATH in n /etc/profile and /usr/local/opt/mysql-client/lib/pkgconfig to PKG_CONFIG_PATH.

I can locate the profile file - but I do not see PATH / PKG_CONFIG_PATH anywhere within the file? Is there an easier way to do it?

hpages commented 3 years ago

Appending /usr/local/opt/mysql-client/bin to the PATH can be done by putting the following line:

export PATH="$PATH:/usr/local/opt/mysql-client/bin"

in /etc/profile.

Then next time you need to append again something to the PATH (e.g. /usr/local/ensembl-vep), replace the above line with:

export PATH="$PATH:/usr/local/opt/mysql-client/bin:/usr/local/ensembl-vep"

And so on.

Same thing for PKG_CONFIG_PATH.

This is basic/generic stuff and our document assumes that the reader is familiar with these things.

H.

hpages commented 3 years ago

Hi @HeikoBre, were you able to solve your problem? If not, please open a new issue so we can discuss it further in the new issue. Closed issue like this one don't receive much attention. Thanks!