Meng's transition
From Informatics
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Revision as of 20:52, 17 June 2014
Contents[hide] |
cluster jobs
Several geworkbench components's backend service is to submit jobs to SGE clusters. They are various different types of software that are mostly NOT part of geworkbench code repository, and similar to each other as cluster jobs from the point of view of the geworkbench application. They are:
- aracne (c++, matlab, perl)
- marina
- demand (R)
- viper (R)
- skyline (perl)
In geworkbench, many of the scripts to be submitted to the cluster are created dynamically created on the control parameters and input data.
Most of them depends on the fact the particular software has been installed on the machine where the script is submitted to the cluster. The machine is afdev in most cases (or all cases?)
Typical, the created script is saved in a sub-directory called 'bin' or 'script', and the corresponding results are saved in sub-directory called 'run'.
Many of them are handled in a similar way concerning how the input data files are transferred for the web service.
web services
The web services developed and maintained by Meng are all Spring framework based, 'wsdl contract-first' web services. Required libraries for the Java clients are: axiom-api-1.2.10.jar and axis2-kernel-1.5.3.jar.
- basic technology: http://docs.spring.io/spring-ws/sites/2.0/reference/html/tutorial.html
- handle large input files: MTOM http://docs.oracle.com/cd/E12840_01/wls/docs103/webserv_adv/mtom.html
aracne
(used by geworkbench web only)
- service code https://github.com/geworkbench-group/aracne.service
- how to submit cluster job? Ken has the ultimate knowledge of this. Q: the commands are just embedded in the aracne service, or documented somewhere else as well?
- what is the account used to do this in geworkbench web? What permission is required for the account, and for the machine to submit qsub, and for what else to make it work?
demand
viper
index service
This is a simplictic index service for other services (demand and viper).
pudge
- contact person: Donald
marina
- contact person?
- remote server information?
- web version
- desktop version
markus
- contact person ??
- remote server information?
skyline
- contact person?
- remote server information?
skybase
- contact person?
- remote server information?
vaadin 7
experience and knowledge
geworkbench1 and geworkbench2
It has been found out that we could not configure two versions both to work properly from outside because of the combination of caTransfer feature and the request redirection from cagridnode. Therefore, there is not much use to maintain two versions.
- how to set proxy during release: modify http.conf file on cagridnode.
gmail account for geworkbench web 'admin'
This is to handle the user registration confirmation message, forget-password request, etc. The actual password should be changed after deployed to the production.
genomespace project
- code base:
- geworkbench component: geonemespace
- geworkbench lauch helper. This is a web start application. The code is not in any version control system. Meng emailed me the latest version in email today (6/17/2014).
- It is deployed on http://www.c2b2.columbia.edu/geworkbench/ (the same server for c2b2 web site), and needed by the genomespace users to launch geworkbench application. Thus, it may need to be updated when we release a new version of geworkbench. The tricky task encountered before is to test it on different OS's and different browsers.
- outside contact: Broad Institute
upgrade cagrid server
This task was pending admin group's work.
