Install SEA: Difference between revisions
No edit summary |
No edit summary |
||
Line 44: | Line 44: | ||
Note that there is a useful manunal distriputed with the source code located in `${seapath}/sea/data/doc/manual.html`. | Note that there is a useful manunal distriputed with the source code located in `${seapath}/sea/data/doc/manual.html`. | ||
Here is the text from SEA_setup.txt: | |||
>>>>>>>>>>>>> Export svn project <<<<<<<<<<<<<< | |||
# wd: ~bet/svn/ | |||
svn co file:///raid4/svn/sea | |||
svn co file:///raid4/svn/sea.molecule | |||
svn co file:///raid4/svn/tanimoto | |||
>>>>>>>>>>>>> Install <<<<<<<<<<<<<< | |||
# wd: ~bet/svn/sea/trunk/ | |||
sudo ./setup.py install | |||
# wd: ~bet/svn/sea.molecule/trunk/ | |||
./setup.py build | |||
sudo ./setup.py install | |||
** Warning: Package missing: daylight ** | |||
>> It just notices that daylight isn't available on your local machine (which is fine because we only have a daylight license for korn) | |||
# wd: ~bet | |||
mkdir public_html | |||
cp -r /usr/arch/share/sea/www/ public_html/sea | |||
cp ~keiser/.sea.cfg . | |||
cp ~keiser/.sea_databases.cfg . | |||
# Change config file | |||
>> SEA database login information | |||
>> [scratch] | |||
>> host=scratch.compbio.ucsf.edu | |||
>> user=bet | |||
>> pass=rubberducky | |||
>> db=bet_sea | |||
cp ~keiser/.sea_molecule* . | |||
rm .sea_molecule.cfg | |||
python /usr/arch/bin/sea-database | |||
>>>>>>>>>>>>> Create database <<<<<<<<<<<<<< | |||
# wd: ~bet | |||
sea-database | |||
create | |||
>>>>>>>>>>>>> Optimize MySQL settings <<<<<<<<<<<<<< | |||
Recommended settings in: /etc/my.cnf | |||
mysql -ubet -p bet_sea -hscratch.compbio.ucsf.edu | |||
>>>>>>>>>>>>>> User manual <<<<<<<<<<<<<<<< | |||
~bet/svn/sea/trunk/data/doc/manual.html | |||
Revision as of 20:49, 14 September 2012
This is intended for Shoichet lab setup. But we hope other find it useful.
The full SEA installation requires a few Python packages:
These are best installed using your distribution's package manager:
yum install scipy numpy atlas atlas-devel mysql mysql-server
On CentOS systems you may need to add an additional repository to make all of these packages available:
wget http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-7.noarch.rpm sudo rpm -Uvh epel-release-6-7.noarch.rpm yum update yum install scipy numpy numpy-f2py atlas atlas-devel mysql mysql-server
The additional web-based results viewer requires:
- Apache
- PHP
- PHP MySQL Libraries
sudo yum install php php-mysql php-cli
You will need to checkout the most recent version of the SEA source code. From within the BKS network this can be done by:
svn co file:///raid4/svn/sea/trunk /tmp/sea
Users outside of the network should see the SEA website for source code availability.
Notes about checkout:
- If you will be installing SEA into the system's Python site-packages the source code will need to be checked out into a location with write access for both the active user account and the local root user, hence `/tmp/sea`.
- It is important that you are using the version of python into which you NumPy and SciPy have been added and which you intent to install SEA to. For example if you wish to install SEA to the local python instance `which python` should return `/usr/bin/python`. If it does not, the easiest way to remidy this is `alias python /usr/bin/python`. This can be the source of many headaches.
Note that there is a useful manunal distriputed with the source code located in `${seapath}/sea/data/doc/manual.html`.
Here is the text from SEA_setup.txt:
>>>>>>>>>>>>> Export svn project <<<<<<<<<<<<<<
- wd: ~bet/svn/
svn co file:///raid4/svn/sea svn co file:///raid4/svn/sea.molecule svn co file:///raid4/svn/tanimoto
>>>>>>>>>>>>> Install <<<<<<<<<<<<<<
- wd: ~bet/svn/sea/trunk/
sudo ./setup.py install
- wd: ~bet/svn/sea.molecule/trunk/
./setup.py build sudo ./setup.py install
- Warning: Package missing: daylight **
>> It just notices that daylight isn't available on your local machine (which is fine because we only have a daylight license for korn)
- wd: ~bet
mkdir public_html cp -r /usr/arch/share/sea/www/ public_html/sea cp ~keiser/.sea.cfg . cp ~keiser/.sea_databases.cfg .
- Change config file
>> SEA database login information >> [scratch] >> host=scratch.compbio.ucsf.edu >> user=bet >> pass=rubberducky >> db=bet_sea
cp ~keiser/.sea_molecule* . rm .sea_molecule.cfg python /usr/arch/bin/sea-database
>>>>>>>>>>>>> Create database <<<<<<<<<<<<<<
- wd: ~bet
sea-database
create
>>>>>>>>>>>>> Optimize MySQL settings <<<<<<<<<<<<<< Recommended settings in: /etc/my.cnf
mysql -ubet -p bet_sea -hscratch.compbio.ucsf.edu
>>>>>>>>>>>>>> User manual <<<<<<<<<<<<<<<< ~bet/svn/sea/trunk/data/doc/manual.html