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bioperl / bioperl-live

Core BioPerl 1.x code
http://bioperl.org
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Unable to run ping_ensembl.pl #353

Open thevinayrao opened 4 years ago

thevinayrao commented 4 years ago

Hi, I followed the instructions mentioned at http://asia.ensembl.org/info/docs/api/api_installation.html to install Ensembl API. At the end, to test the installation, we are to run the test file ping_ensembl.pl. At this stage, I am constantly receiving the following error -

Error detected when connecting to Ensembl! Looks like you need to setup your PERL5LIB with BioPerl.

I have followed the video guide to install it, and I have also updated ~/.profile

Below are the changes made in ~/.profile

export PERL5LIB=/home/vinay/softwares/ensembl_vep/ensembl/modules:$PERL5LIB export PERL5LIB=/home/vinay/softwares/ensembl_vep/ensembl-variation/modules:$PERL5LIB export PERL5LIB=/home/vinay/softwares/ensembl_vep/ensembl-compara/modules:$PERL5LIB export PERL5LIB=/home/vinay/softwares/ensembl_vep/ensembl-funcgen/modules:$PERL5LIB export PERL5LIB=/home/vinay/softwares/ensembl_vep/ensembl-tools/modules:$PERL5LIB export PERL5LIB=/home/vinay/softwares/ensembl_vep/bioperl/bioperl-live-master/modules:$PERL5LIB export PERL5LIB

Any help would be appreciated.

Thank you

cjfields commented 3 years ago

@thevinayrao that directory setup looks wrong (our modules are in the standard lib directory), maybe try:

export PERL5LIB=/home/vinay/softwares/ensembl_vep/bioperl/bioperl-live-master/lib:$PERL5LIB

You can test whether this is in your path by running something like perldoc -l Bio::Root::Root after you restart the shell, it should tell you the location of the Bio::Root::Root module in your PERL5LIB path

$ perldoc -l Bio::Root::Root
/Users/cjfields/bioperl/bioperl-live/lib/Bio/Root/Root.pm
carandraug commented 3 years ago

This issue seems to be on the ensembl documentation. You should really be using some sort of package manager to install perl module distributions, possibly cpanm but maybe also your OS package manager. If you just download the source releases and add the modules to the path, you're likely to end up with a broken "installation".

I'd close this as invalid.