This directory contains the materials needed to construct a working Shrimp workflow, with some example data.
If you have not done so already, please clone this example repository like so:
git clone https://github.com/cooperative-computing-lab/makeflow-examples.git
cd ./makeflow-examples/shrimp
First, obtain a rmapper-cs binary suitable for your architecture
from compbio.cs.toronto.edu/shrimp. (At the time of writing,
this website was offline, so a rmapper-cs binary for Linux-x86
is currently included in the repository.)
If you need some example data to work with, download this to
obtain genome.fasta and query.csfasta:
wget http://ccl.cse.nd.edu/workflows/shrimp-example-data.tar.gz
tar xvzf shrimp-example-data.tar.gz
Test the rmapper-cs executable to make sure that it works locally:
./rmapper-cs -M fast -M 50bp query.csfasta genome.fasta
If that works, you can construct a workflow to parallelize it:
./make_shrimp_workflow query.csfasta genome.fasta output.txt 10000 > shrimp.mf
Then, you can use makeflow to run the whole thing as desired.
For example, to run it all locally:
makeflow shrimp.mf
Or to run it using HTCondor or Work Queue or SGE:
makeflow -T condor shrimp.mf
makeflow -T wq shrimp.mf
makeflow -T sge shrimp.mf
Alternatively, it can be run using the JX or JSON format
makeflow --jx shrimp.jx
makeflow --json shrimp.json
To visualize the workflow that was generated:
makeflow_viz shrimp.mf --dot-no-labels > shrimp.dot
dot -Tpng shrimp.dot > shrimp.png
display shrimp.png