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ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
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Error during install #73

Closed linsalrob closed 13 years ago

linsalrob commented 13 years ago

Still not getting install to work. This is on a relatively clean 64-bit linux with no FIG system available.

redwards@goldeneye:/data/ModelSeed$ git pull Already up-to-date. redwards@goldeneye:/data/ModelSeed$ cat config/MySettings.config 

[Database]
# type is either sqlite or mysql
type=sqlite

# required for sqlite
filename=/data/ModelSeed/databases/db.sqllite

# required for mysql
# username=
# password=
# host=
# socket=
# port=

     [Optional]

dataDirectory==/data/ModelSeed/data/

     [Optimizers]

admin_users=admin1,admin2: this configuration is no longer in use and can be deleted

includeDirectoryGLPK=/usr/include
libraryDirectoryGLPK=/usr/lib
# includeDirectoryCPLEX=
# libraryDirectoryCPLEX=
# licenceDirectoryCPLEX=
redwards@goldeneye:/data/ModelSeed$ ./bin/ms-config load config/MySettings.config

Your configuration file was adjusted based on changes made to the installation process. Please check the file!

[: 4: unexpected operator g++ -O3 -fPIC -fexceptions -DNDEBUG -DIL_STD -DILOSTRICTPOD -DLINUX -I../Include/ -DNOSAFEMEM -DNOBLOCKMEM -I/usr/include -o /data/ModelSeed/software/mfatoolkit/Linux/mfatoolkit /data/ModelSeed/software/mfatoolkit/Source/driver.o /data/ModelSeed/software/mfatoolkit/Source/MFAProblem.o /data/ModelSeed/software/mfatoolkit/Source/CPLEXapiEMPTY.o /data/ModelSeed/software/mfatoolkit/Source/SCIPapi.o /data/ModelSeed/software/mfatoolkit/Source/GLPKapi.o /data/ModelSeed/software/mfatoolkit/Source/LINDOapiEMPTY.o /data/ModelSeed/software/mfatoolkit/Source/SolverInterface.o /data/ModelSeed/software/mfatoolkit/Source/Species.o /data/ModelSeed/software/mfatoolkit/Source/Data.o /data/ModelSeed/software/mfatoolkit/Source/InterfaceFunctions.o /data/ModelSeed/software/mfatoolkit/Source/Identity.o /data/ModelSeed/software/mfatoolkit/Source/Reaction.o /data/ModelSeed/software/mfatoolkit/Source/GlobalFunctions.o /data/ModelSeed/software/mfatoolkit/Source/AtomCPP.o /data/ModelSeed/software/mfatoolkit/Source/UtilityFunctions.o /data/ModelSeed/software/mfatoolkit/Source/AtomType.o /data/ModelSeed/software/mfatoolkit/Source/Gene.o /data/ModelSeed/software/mfatoolkit/Source/GeneInterval.o /data/ModelSeed/software/mfatoolkit/Source/stringDB.o -L/usr/lib -lglpk ""Unable to find database configuration for ModelDB USERS"" at /data/ModelSeed/lib/ModelSEED/FIGMODEL.pm line 136 ModelSEED::FIGMODEL::FIGMODELERROR('Unable to find database configuration for ModelDB USERS') called at /data/ModelSeed/lib/ModelSEED/FIGMODEL/FIGMODELdatabase.pm line 158 ModelSEED::FIGMODEL::FIGMODELdatabase::get_object_manager('ModelSEED::FIGMODEL::FIGMODELdatabase=HASH(0x28c6d28)', 'user') called at /data/ModelSeed/lib/ModelSEED/FIGMODEL/FIGMODELdatabase.pm line 272 ModelSEED::FIGMODEL::FIGMODELdatabase::sudo_get_objects('ModelSEED::FIGMODEL::FIGMODELdatabase=HASH(0x28c6d28)', 'user', 'HASH(0x28c6a10)') called at /data/ModelSeed/lib/ModelSEED/FIGMODEL/FIGMODELdatabase.pm line 298 ModelSEED::FIGMODEL::FIGMODELdatabase::get_objects('ModelSEED::FIGMODEL::FIGMODELdatabase=HASH(0x28c6d28)', 'user', 'HASH(0x28c6a10)') called at /data/ModelSeed/lib/ModelSEED/FIGMODEL/FIGMODELdatabase.pm line 249 ModelSEED::FIGMODEL::FIGMODELdatabase::get_object('ModelSEED::FIGMODEL::FIGMODELdatabase=HASH(0x28c6d28)', 'user', 'HASH(0x28c6a10)') called at /data/ModelSeed/bin/../lib/ModelSEED/ModelSEEDScripts/ms-config.pl line 392

devoid commented 13 years ago

I think your database schema is out of date.

Try downloading a new copy of the database from: http://bioseed.mcs.anl.gov/~devoid/ModelDB-sqlite.tgz

And extracting it:

tar -xzf ModelDB-sqlite.tgz -C /root/data/

where /root/data/ is your data directory

Then loading the sqlite dump into a database:

sqlite3 /root/data/ModelDB/ModelDB.db < /root/data/ModelDB/ModelDB.sqlite
linsalrob commented 13 years ago

Wow, that gave me massive amounts of errors, mainly that alias, type, REACTION are not unique.

However, that, together with changing the config line: filename=/data/ModelSeed/databases/db.sqllite to filename=/data/ModelSeed/data/ModelDB/ModelDB.db

successfully installed the database. I'm going to consider this closed,

Thanks!!

Rob

devoid commented 13 years ago

Oh, sorry. The instructions I gave you neglected to mention deleting or moving the ModelDB.db file before doing the sqlite3 load step. The errors are occurring because most rows are being inserted twice (or at least trying to). If you repeat those steps after moving the old database all should be good.