Question: Orthomcl install schema error
0
gravatar for max_19
5 months ago by
max_19110
max_19110 wrote:

Hi all!

I'm trying to run Orthomcl, I got to step 4 ( http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt ) however running orthomclInstallSchema keeps resulting in an error for me. Below is my code and error message:

orthomclInstallSchema my_orthomcl_dir/orthomcl.config my_orthomcl_dir/install_schema.log

Can't locate DBD/mysql.pm in @INC (you may need to install the DBD::mysql module)

Here is my orthomcl.config file:

dbVendor=mysql 
dbConnectString=dbi:mysql:mmax_orthomcl
dbLogin=mmax
dbPassword=PASSWORD
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-3
oracleIndexTblSpc=NONE

I tried manually installing DBD::mysql using code below, and I get another error about Devel::CheckLib

[DBD-mysql-4.050]$ perl Makefile.PL

Can't locate Devel/CheckLib.pm in @INC (you may need to install the Devel::CheckLib module)

Has anyone encountered this when trying to run Orthomcl? any help is appreciated. Thank you.

ADD COMMENTlink written 5 months ago by max_19110
1

Did you try installing DBD::mysql with cpan (or cpanm)?

ADD REPLYlink written 5 months ago by h.mon27k

I just tried that, however I still get an error (but now it's a different error):

$ orthomclInstallSchema my_orthomcl_dir/orthomcl.config my_orthomcl_dir/install_schema.log

can't find property dbname in config file

my config file is posted above, and when i go into mysql, I can see the database that I created:

mysql> SHOW DATABASES;

+--------------------+
| Database           |
+--------------------+
| information_schema |
| mmax_orthomcl     |
+--------------------+
2 rows in set (0.00 sec)
ADD REPLYlink modified 5 months ago • written 5 months ago by max_19110
0
gravatar for ATpoint
5 months ago by
ATpoint21k
Germany
ATpoint21k wrote:
 conda install -c bioconda orthomcl
ADD COMMENTlink written 5 months ago by ATpoint21k
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