Online update is a key feature of ABCGrid, which is used to install and update all bioinformatics applications and databases in worker nodes automatically. Online update use File Transfer Protocol (FTP) to download all necessary files from a FTP server. For example, ABCGrid can access public databases. However, a better way to A demo layout of FTP server:
FTP_root
|
|---NCBI
|
|---executable
|
|---blast-2.2.14-axp64-tru64.tar.gz
|---blast-2.2.14-ia32-freebsd.tar.gz
|---blast-2.2.14-ia32-linux.tar.gz
|--- ...
|---db
|
|---nr.00.tar.gz
|---nr.01.tar.gz
|---nt.00.tar.gz
|---nt.01.tar.gz
|--- ...
|---HMMER
|
|---executable
|
|---hmmer-2.3.2-amd64-linux.tar.gz
|---hmmer-2.3.2-x86-linux.tar.gz
|--- ...
|---db
|---Pfam_ls.gz
|---Pfam_fs.gz
This layout of FTP server is very similiar with NCBI's ftp site for blast.
The path "NCBI" and "HMMER" are names of bioinformatics services.
Under each services, there should be one directory named "executable" and one directory "db" (if databases are needed).
The files under directory "executable" should be executable files,
Each component must be compressed using .gz, .zip, .tar.gz or a self-extracted .exe file.