The Docking Gateway is a Liferay portlet aimed to work together with gUSE/WSPGRADE. It provides access to distributed computing resources (grid, PBS, SGE, ...) to biochemists working on molecular docking.
The portlet requires a user and scheme on a MySQL server.
git clone https://github.com/AMCeScience/docking-gateway.git docking
cd docking
mvn -s ./ebioinfra.settings.xml package
autodock.war
file can be found on docking/target
autodock.war
fileDockingAdmin
roleautodock
porlet in the new pageFor a local deployment where the WebDAV repository and Liferay instance run on the same machine, WebDAV relies on the Liferay user credentials for athentication. Also, two different WebDAV context are provided:
The proposed authentiation scheme is based on mod_auth_mysql
and Apache >=2.2 server. The Apache configuration is as follows:
# public WebDAV context
Alias /webdav "path/repository"
# private localhost-only WebDAV context
Alias /webdav-curl "path/repository"
# WebDAV configuration
<Location /webdav>
DAV On
AuthBasicAuthoritative Off
AuthUserFile /dev/null
AuthMySQLEnable On
AuthName "webdav"
AuthType Basic
AuthMySQLHost localhost
AuthMySQLUser liferay
AuthMySQLPassword liferay.password
AuthMySQLDB liferay
AuthMySQLUserTable User_
AuthMySQLNameField emailAddress
AuthMySQLPasswordField password_
AuthMySQLNoPasswd Off
AuthMySQLPwEncryption sha1
AuthMySQLAuthoritative On
require valid-user
</Location>
# WebDAV configuration, local context
<Location /webdav>
DAV On
AuthBasicAuthoritative Off
AuthUserFile /dev/null
AuthMySQLEnable On
AuthName "webdav"
AuthType Basic
AuthMySQLHost localhost
AuthMySQLUser liferay
AuthMySQLPassword liferay.password
AuthMySQLDB liferay
AuthMySQLUserTable User_
AuthMySQLNameField emailAddress
AuthMySQLPasswordField password_
AuthMySQLNoPasswd Off
AuthMySQLPwEncryption sha1
AuthMySQLAuthoritative On
require valid-user
</Location>
To make possible for mod_auth_mysql
module to authenticate against Liferay User database, it is required to change the hasshing algorithm and encoding used by default by Liferay. The above authentication scheme would require the following options on $HOMELIFERAY/porta-ext.properties
:
passwords.encryption.algorithm=SHA
passwords.digest.encoding=hex
autodock_files
config.json
and the ligand libraries in this folder/autodock_files/ligands/[library name]/[ligand files]
Official Docking Gateway documentation https://docking.ebioscience.amc.nl/portal/documentation
For further information and details, contac us at:
support-nsg[at]ebioscience[dot]amc[dot]nl