1 CDL for BLAST based on Chris’s JSDL document* OGSA-WG 14 March, 2006 *:

2 BLAST command blastall -p blastn -d est -F T -F Filter[String] If one uses "-F T" then normal filtering occurs. -d Database [String] Input could be one of "/db/ncbiblast/nr", "/db/ncbiblast/nt", "/db/ncbiblast/est" or user own database. -p Program Name [String] Input should be one of "blastp", "blastn", "blastx", "tblastn", or "tblastx". Question: Who sets up this est database?

3 CDL document includes 1.Application binary installation If this application depends on specific libraries or other software, how to deploy them should be described by CDL 2.File system mount /usr/local/bin/blastall temporary … normal Chris's home directory /home/csmith Alternative: JM selects container which already mounts these file systems

4 CDL document may include 3.Set environment variables /usr/bin:/usr/local/bin:/usr/local/bio/bin Alternative: BES container sets them when job is initiated

5 CDL document does not include 1.Job Identification 2.Application Name and version May be used to identify CDL document 3.Resource types Except FileSystem 4.Posix argument & stdin/stdout/stderr BES container does when job is initiated 5.Change working directory BES container does when job is initiated 6.Set hard/soft limit BES container does when job is initiated 7.User & Group JM selects container already has specified user 8.Stage / destage data file BES container does

6 JSDL:JobDescription Does not included maybe Included in CDL PosixApplication See slide 5 See slide 6 Stage/destage Data file

7 JSDL:PosixApplication Does not included maybe Included in CDL Application binary Hard/soft limit User & group Working directory Environment Variable

8 JSDL:Resource Does not included maybe Included in CDL File system mount