Hello,
I have installed anaconda3 on Ubuntu 16.04.3 LTS, and have installed
the rdkit-postgresql95
conda environment.
When trying to install the cartridge on a new db, I get the message -
ERROR: could not open extension control file "/home/drew/anaconda3/envs/
rdkit/share/postgresql/extension/rdkit.control": No such file or directory
Sequence of commands to install and set-up (error occurs after the last
command)...
NB, when I do the following with the standard rdkit-postgresql package, I
don't get the error.
// having installed anaconda3, install the rdkit-postgresql95 conda
environment
// rdkit: 2017.09.1-py35_1 rdkit
// rdkit-postgresql95: 2016.09.4-py35_1 rdkit
conda create -c rdkit -n rdkit rdkit-postgresql95
// create the directory for postgres data
mkdir ~/anaconda3/envs/rdkit/pgdata
// activate the environment
source activate rdkit
// navigate to the /bin directory
cd ~/anaconda3/envs/rdkit/bin
// run initdb
./initdb ~/anaconda3/envs/rdkit/pgdata
// initdb creates postgres.conf in the /pgdata folder -
// we can now edit to rdkit recommended settings.
"To improve performance while loading the database and building the
index, I changed a
couple of postgres configuration settings in postgresql.conf :"
synchronous_commit = off # immediate fsync at commit
full_page_writes = off # recover from partial page writes
"And to improve search performance, I allowed postgresql to use more
memory than the
extremely conservative default settings:"
shared_buffers = 2048MB # min 128kB (change requires restart)
work_mem = 128MB # min 64kB
// reboot (to new config), activate the environment then start the DB
server from /bin
./pg_ctl -D /home/drew/anaconda3/envs/rdkit/pgdata -l logfile start
// navigate to the /bin directory and create chembl DB
./createdb chembl_23
// back out to command line and setup rdkit cartridge on db
./psql -c 'create extension rdkit' chembl_23
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