Annot8r installation. To configure postgresSQL for ... - The GenePool

boreddizzyΔιαχείριση Δεδομένων

16 Δεκ 2012 (πριν από 4 χρόνια και 7 μήνες)

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Annot8r installation.
To configure
postgresSQL for
annot8r:
1) Install packages:
To run
annot8r on
lymnaea,the following had to be installed using
sudo
yuminstall:
perl-bioperl
perl-DBD-Pg.x86-64
wget
postgresql.x86_64
postgresql-server.x86_64
php-pgsql.x86_64
Logged in as root user,or using the
sudo command
On Fedora/Red hat
linux:
yum install
perl-bioperl
perl-DBD-Pg.x86-64 etc...
On
Ubuntu or
Debian
Linux,use:
apt-get install
perl-bioperl
perl-DBD-Pg.x86-64 etc...
2) To configure
postgres
SQL
sudo
/sbin/chkconfig
postgresql on
sudo
/sbin/service
postgresql
initdb
sudo
/sbin/service
postgresql start
su
su
postgres
psql
template1
create user
john
createdb
createuser;
\q
Alternatively the following commands can be used:
sudo
su -
postgres
[enter my password]
[changes to bash prompt:bash-4.0$]
psql
template1
\
du (lists current users/roles)
create user
stella
createdb
createuser;(remember the semi-colon at the end) (creates user with
superuser permissions which seemto be needed by
annot8r)
\
du (list users to confirm)
\q (exits)
Other useful commands:
\l (lists all databases)
To create a new database,use:
CREATE DATABASE"2009057_Project_Name”;
(remember the quotes and semi-colon at the end.)
Running
Annot8r:
To start,type:
annot8r.pl
Choose:
1.Download relevant files
4.Download everything
2.Extract data fromfiles into databases
4.Create or update all of them
3.Prepare your BLAST searches
4.Create all of them
Using the System-->Administration-->
SELinux tool
On the Boolean tab,I ticked the box to give access to “
exim” and “
userdomain”
There may also be permissions to set with the systemtool on
lymnaea as
SELinux can restrict
acccess for security.
May need to delete the
'/tmp/temp_
goa_
uniprot'file fromthe
/tmp directory as cannot overwrite if it
was created by another user.- BUT this is no longer used in my updated version 1.1.3 of the script
which
COPYs from
STDIN,when importing the data to the databases now.