Tips In Setting Up Oshell

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The libraries required for oshell are:

  • Mono, must compile from source with --with-large-heap=yes, version 4.10.4 or above.
  • Libgdiplus, make sure libgdiplus.so is accessible in cluster nodes. Add LD_LIBRARY_PATH “export LD_LIBRARY_PATH=/pathtolibgdiplus/folder:$LD_LIBRARY_PATH” in every cluster node. If it is too much trouble to add the path. You add this line in every bsub/qsub script before the oshell line if it is running in a cluster.
  • zlib-devel package must be installed in every node.

We would suggest you having a folder with the following structure:

/Omicsoft
--/Mono
--------/mono-6.10.0.104
-----------------/bin
--------/mono-6.10.0.104
-----------------/bin
--/libgdiplus
--------/libgdiplus-2.10
--/Oshell
--------oshell.exe
--------OmicsoftUpdater.exe
--OmicsoftHome

You may use new mono versions later. You can keep them in the same Mono master folder. OmicsoftHome folder is used as the base dir for Oshell runs which storing ReferenceLibrary and temp folder if Temp_Dir is not specified in oshell runs.

If it is running in a cluster, you have to make sure that the whole Omicsoft folder is accessible in all cluster node. It is also a good idea to have a local scratch space in each machine node with the same folder path to store temp files during Oshell runs.

Also Read

Getting started with Oshell