Question: Orthomcl install schema error
0
gravatar for max_19
28 days ago by
max_1950
max_1950 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 28 days ago by max_1950
1

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

ADD REPLYlink written 28 days ago by h.mon24k

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 28 days ago • written 28 days ago by max_1950
0
gravatar for ATpoint
27 days ago by
ATpoint15k
Germany
ATpoint15k wrote:
 conda install -c bioconda orthomcl
ADD COMMENTlink written 27 days ago by ATpoint15k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 933 users visited in the last hour