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cdanielmachado / transcript2flux

Scripts and results from omics-based methods assessment paper in PLoS Comp Bio 2014
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Add support for MADE via TIGER toolbox #3

Open bbarker opened 10 years ago

bbarker commented 10 years ago

This is mainly a reminder for me or someone else to hopefully add this feature if given time.

Currently an older version of gurobi is required for the version of MADE included in transcript2flux; it would be good to have the same version of gurobi used in all tests (if nothing else this simplifies installation greatly) MADE is now part of the TIGER toolbox (bitbucket.org/csbl/tiger), which supports Gurobi5 as of version 1.3.

See https://bitbucket.org/paj2s/made/issue/1/cmpi-doesnt-support-gurobi5 for more details.

cdanielmachado commented 10 years ago

Thanks for the reminder.

Indeed it would make more sense to use the new version in the TIGER toolbox (that would solve the gurobi issue as well). However, in this case the decision was to keep as close as possible to original publication (since this is a review paper after all).

I'll try to update to the new version if I find some time to do it. Otherwise, please feel free to contribute with the update yourself when you get a chance to do it :)