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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
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Error: when install Variant Effect Predictor #107

Closed jianzuoyi closed 7 years ago

jianzuoyi commented 7 years ago

I installed the Variant Effect Predictor as follows (This instructions were shown in the home page of SpeedSeq):

curl -OL https://github.com/Ensembl/ensembl-tools/archive/release/76.zip unzip 76.zip perl ensembl-tools-release-76/scripts/variant_effect_predictor/INSTALL.pl \ -c $SPEEDSEQ_DIR/annotations/vep_cache \ -a ac -s homo_sapiens -y GRCh37

cp ensembl-tools-release-76/scripts/variant_effect_predictor/variant_effect_predictor.pl $SPEEDSEQ_DIR/bin cp -r Bio $SPEEDSEQ_DIR/bin

Update the VEP and VEP_CACHE_DIR variables in speedseq.config to point to

$SPEEDSEQ_DIR/bin/variant_effect_predictor.pl and $SPEEDSEQ_DIR/annotations/vep_cache

But the 'INSTALL.pl ' has some errors when I run this command: perl ensembl-tools-release-76/scripts/variant_effect_predictor/INSTALL.pl \ -c $SPEEDSEQ_DIR/annotations/vep_cache \ -a ac -s homo_sapiens -y GRCh37'

I found that the 'INSTALL.pl' script need 'BioPerl-1.6.1.tar.gz', but the url 'http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz' is not exist.The installation of VEP failed.

Any solutions for this problem? thank you very much.

cc2qe commented 7 years ago

It looks like bioperl has changed their installation procedure. I'd recommended referring to the VEP installation page and running the installation commands there:

curl -L -O https://github.com/Ensembl/ensembl-vep/archive/release/88.zip
unzip 88.zip
cd ensembl-vep-release-88/

followed by:

perl ensembl-vep-release-88/INSTALL.pl \
    -c $SPEEDSEQ_DIR/annotations/vep_cache \
    -a ac -s homo_sapiens -y GRCh37
jianzuoyi commented 7 years ago

Thanks very much for your answer. My problems is solved, and I'm going to close this issue.