I have been struggling with the analysis of data on OrthoMCL program and it always come up with the issue as follows when the analysis arrive at the "orthomclInstallSchema" step. In addition, I have confirmed that DBI and DBD::mysql have been installed already.
The command line is:
orthomclInstallSchema orthomcl.config install_schema.log
The reported error is:
DBI connect('orthomcl:3307','orthomcl',...) failed: Can't connect to MySQL server on '3307' (22) at ../lib/perl/OrthoMCLEngine/Main/Base.pm line 56
The content in orthomcl.config:
dbVendor=mysql dbConnectString=dbi:mysql:orthomcl:3307 dbLogin=orthomcl dbPassword=XXXXXXX similarSequencesTable=SimilarSequences orthologTable=Ortholog inParalogTable=InParalog coOrthologTable=CoOrtholog interTaxonMatchView=InterTaxonMatch percentMatchCutoff=50 evalueExponentCutoff=-5 oracleIndexTblSpc=NONE
Any solution to get around this?