search

hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
http://hallam.microbiology.ubc.ca/MetaPathways/
33 stars 14 forks source link

Documentation on grid setup #57

Closed rpelicae closed 7 years ago

rpelicae commented 9 years ago

Hello, I want to try to use MetaPathways 2.5 where I perform the FUNC_SEARCH step on a remote compute cluster.

  1. In the documentation of MetaPathways 1 it is said that computational tasks can be externalized providing the cluster uses the Sun Grid Engine scheduler. Is it for MetaPathways 2.5 possible to externalize to a cluster that uses TORQUE/Moab?
  2. I understand that the cluster I want to use needs the blastp binary and the functional databases I want to search on. Is there a way to use the same configuration file as if I wanted to run the pipeline locally, i.e. without hard-coding the path to binaries and files each time?
  3. Is there any manual intervention needed when one wants to externalize different steps of the pipeline, e.g. FUNC_SEARCH and MLTREEMAP_CALCULATION? How does the I/O work in MetaPathways when you externalize tasks?

Hope to hear from you, Kind regards, Rudy

hallamlab commented 7 years ago

we are moving toward using docker for MP - we are building a version should be easily used on multiple systems. I hope the new upcoming version will solve these problems