Imicrobe:iPlant integration

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Contents

List of Apps in iPlant

Gene Finding Programs:

Glimmer (Glimmer-1.0.0)
Prodigal (Prodigal 2.5)
Metagene (MetaGeneAnnotator-1.0.0)

Assembly Programs:

Metavelvet (Metavelvet-1.0.0)
SPA (SPA-1.0.0)
IDBA-UD (IDBA-UD-1.0.0)
Mummer (Mummer)

Utility Programs:

Genome-tools (k-mer based tools)
BuildICM-1.0.0-Dev

Existing Tools in iPlant useful for metagenomics:

Newbler assembler
Soap-de-novo
Velvet
Abyss
FragGeneScan
MetaPhyler
Krona Tools
MetaPhlan
MetaGenemark


Steps to run apps in iPlant

1) login to discovery environment - http://www.iplantcollaborative.org/discover/discovery-environment

2) Goto apps icon on the left hand side ( lhs ) pane.

3) There is a category tree on the left side of the window. Select "iMicrobe" folder in "Public Apps".

4) From the list, search any app, say Prodigal, select the app row and click on the first icon ( will show "run" on mouse hover ) besides "create" button.

5) This will popup app GUI, fill in the required inputs and hit "Launch Analysis" on the rightmost bottom corner of the popped window.

6) Fill in any name for analysis run and check retain inputs.

7) After that you will get notification on the rightmost top corner of the iPlant page.

8) You can monitor the status of analysis by clicking on "Analyses" on lhs pane and hitting refresh button intermittently.

9) Once job will be finished, you can browse the output files or error files by clicking on analysis name. Final notification of failure or completion will be sent on registered e-mail as well.

irods settings for iPlant

Host name (DNS) of server to which to connect - data.iplantcollaborative.org
Port number - 1247
iRODS user name - <your iplant login name>
iRODS zone - iplant
Current iRODS password - <your iplant password>

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