[ensembl-dev] Error in dump_transcripts.pl from the blog post Human BodyMap 2.0 data from Illumina
th3
th3 at sanger.ac.uk
Fri Aug 24 15:15:34 BST 2012
Hi Jerry,
You need bioperl in your PERL5LIB.
We are using bioperl-1.2.3 so I would recommend you to use this one.
(But the newest bioperl should work too)
Hope this help
Thibaut
==============================================================
I ran the script dump_transcripts.pl listed above and got a whole bunch
of errors such as those listed below. Does the new release of Ensembl 68
have something to do with it where modules were changed? I re-installed
Emsembl API but it still doesn’t work. Perhaps the name of the modules
changed thus they need to be changed in the script as well? Please
advice. Thank you!
Error Output:
——————– WARNING ———————-
MSG: ‘Bio::EnsEMBL::DBSQL::GeneAdaptor’ cannot be found.
Exception Can’t locate Bio/PrimarySeqI.pm in @INC (
BEGIN failed–compilation aborted at
/home/jli/src/ensembl/modules/Bio/EnsEMBL/Slice.pm line 62.
Compilation failed in require at
/home/jli/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 99.
BEGIN failed–compilation aborted at
/home/jli/src/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm line 99.
Compilation failed in require at
/home/jli/src/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm line 67.
BEGIN failed–compilation aborted at
/home/jli/src/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm line 67.
Compilation failed in require at (eval 8) line 3.
FILE: Bio/EnsEMBL/Registry.pm LINE: 1015
CALLED BY: dump_transcripts.pl LINE: 88
Date (localtime) = Thu Aug 23 16:54:56 2012
Ensembl API version = 68
Jerry
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