Galaxy error log file reports a few problems with sqllite (locking) - even with a single user installation.
Attempt to resolve: install Postgres as the database (sorry, this is a bit disjointed - we did this a while ago)
Modify the line in the universe_wsgi.ini file to tell galaxy to use a local psql database:
postgres://galaxy:galaxy@localhost/galaxy_data
less /var/log/galaxy.log indicates that it can't see psycopg2
Install psycopg2 from synaptic doesn't work (understandably) so attempt to install as follows:
python /usr/lib/galaxy-server/scripts/fetch_eggs.py
Reports problems finding the eggs:
ImportError: No module named psycopg2...
so get the egg manually:
simonw@pc024055-AlvaroGroup[eggs] sudo wget http://eggs.g2.bx.psu.edu/psycopg2/psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg [10:41AM]
[sudo] password for simonw:
--2012-08-30 10:41:35-- http://eggs.g2.bx.psu.edu/psycopg2/psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg
Resolving eggs.g2.bx.psu.edu... 128.118.200.135, 2610:8:7800:14::42
Connecting to eggs.g2.bx.psu.edu|128.118.200.135|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 323763 (316K) [text/plain]
Saving to: `psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg'
100%[===================================================================================================================================================================================================>] 323,763 363K/s in 0.9s
2012-08-30 10:41:36 (363 KB/s) - `psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg' saved [323763/323763]
simonw@pc024055-AlvaroGroup[eggs] less psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg [10:41AM]
"psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg" may be a binary file. See it anyway?
simonw@pc024055-AlvaroGroup[eggs] unzip -v pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg [10:41AM]
simonw@pc024055-AlvaroGroup[eggs] unzip -v psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg [10:41AM]
Archive: psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg
100%[===================================================================================================================================================================================================>] 323,763 363K/s in 0.9s
2012-08-30 10:41:36 (363 KB/s) - `psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg' saved [323763/323763]
simonw@pc024055-AlvaroGroup[eggs] less psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg [10:41AM]
"psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg" may be a binary file. See it anyway?
simonw@pc024055-AlvaroGroup[eggs] unzip -v pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg [10:41AM]
simonw@pc024055-AlvaroGroup[eggs] unzip -v psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg [10:41AM]
Archive: psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg
run sh manage_db.sh upgrade to resolve problems with existing schema.
