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Probelm installing vep with conda #1378

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abalter opened this issue Mar 16, 2023 · 4 comments
Closed

Probelm installing vep with conda #1378

abalter opened this issue Mar 16, 2023 · 4 comments
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@jamie-m-a

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@abalter
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abalter commented Mar 16, 2023

Describe the issue

I created a fresh conda environment. I installed vep with micromamba install -c bioconda ensembl-vep. (I already have conda-forge and bioconda in that order in my .condarc, but figured I'd be specific.) I got no installation errors. However vep will not run properly.

Additional information

See below for error.

System

  • VEP version: [e.g. 98 or 98.1]
  • VEP Cache version: [e.g. 98]
  • Perl version: [e.g. 5.26] 5.32.1
  • OS: [e.g. MacOS, Ubuntu, CentOS] CentOS
  • tabix installed ? No, but I could

For VEP version:

(vep) balter@spectre:~$ conda list | grep vep
List of packages in environment: "/home/balter/micromamba/envs/vep"
  ensembl-vep                            109.3            pl5321h4a94de4_0        bioconda

Full VEP command line

(vep) balter@spectre:~$ which vep
/home/balter/micromamba/envs/vep/bin/vep
(vep) balter@spectre:~$ vep -V
Compress::Raw::Zlib version 2.201 required--this is only version 2.105 at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/Compress/Zlib.pm line 11.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/Compress/Zlib.pm line 11.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 89.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 89.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
Compilation failed in require at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 100.
        ...propagated at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 109.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
Compilation failed in require at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 100.
        ...propagated at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 109.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
Compilation failed in require at /home/balter/micromamba/envs/vep/bin/vep line 20.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/bin/vep line 20.
(vep) balter@spectre:~$ vep --version
Compress::Raw::Zlib version 2.201 required--this is only version 2.105 at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/Compress/Zlib.pm line 11.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/Compress/Zlib.pm line 11.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 89.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 89.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
Compilation failed in require at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 100.
        ...propagated at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 109.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
Compilation failed in require at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 100.
        ...propagated at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 109.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
Compilation failed in require at /home/balter/micromamba/envs/vep/bin/vep line 20.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/bin/vep line 20.
(vep) balter@spectre:~$ vep -h
Compress::Raw::Zlib version 2.201 required--this is only version 2.105 at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/Compress/Zlib.pm line 11.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/Compress/Zlib.pm line 11.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 89.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 89.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
Compilation failed in require at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
Compilation failed in require at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 100.
        ...propagated at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 109.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
Compilation failed in require at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 100.
        ...propagated at /home/balter/micromamba/envs/vep/lib/perl5/site_perl/base.pm line 109.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/share/ensembl-vep-109.3-0/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
Compilation failed in require at /home/balter/micromamba/envs/vep/bin/vep line 20.
BEGIN failed--compilation aborted at /home/balter/micromamba/envs/vep/bin/vep line 20.
@jamie-m-a
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jamie-m-a commented Mar 17, 2023 •
edited
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Hi @abalter

We don't support conda installs of VEP as they are not packages created by us. If you have a strong desire to use a conda install of VEP it's best to seek help from the creator of the package.

Alternatively we do provide an extensive docker image which we fully support, details are available on our download page here - scroll down to the Docker section.

@barslmn
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barslmn commented Mar 22, 2023

I was testing for something else and need to install VEP with conda. It might be helpful for you too. Here is the colab example:

https://colab.research.google.com/drive/1pJ4RejOPlkSlQOIhHM2JNd0jalC7UWuV?usp=sharing

@dinglinfeng
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update the perl package works for me.
mamba update -c conda-forge perl-compress-raw-zlib

@jamie-m-a
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Closing this issue down now, please reach out to us if you have any more questions.

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@abalter @barslmn @jamie-m-a @dinglinfeng