modelseed / mfatoolkit Goto Github PK

I keep getting this error when running FBA/gapfilling:

'mkdir: cannot create directory `/tmp/fbajobs/nMekMbBbJ5/MFAOutput': File exists'

It's not a serious error, but it's a bit misleading, would be nice if we could fix it.

Is there any documentation for this software?

We should use standard tools for configuring/installing MFAToolkit.

Right now to compile MFAToolkit from a locally installed glpk, here are the commands:

INC="-I/homes/pfrybar/public_html/msdist/test/local/include -L/homes/pfrybar/public_html/msdist/test/local/lib" LD_RUN_PATH=/homes/pfrybar/public_html/msdist/test/local/lib make
TARGET=/homes/pfrybar/public_html/msdist/test/local/ make deploy-mfatoolkit

If we do this correctly then all we have to do is:

./configure --prefix=/homes/pfrybar/public_html/msdist/test/local
make
make install

A minor issue - the configuration complains if MFATK_BIN is not set:

MFATK_BIN configuration is undefined!
This is the directory that contains the mfatoolkit binary. If it
is not already installed, this program can be downloaded from:
https://github.com/modelseed/mfatoolkit
Add the binary directory to your path or use the following command:

$ ms config MFATK_BIN=VALUE

However, this should be set to the path to the executable not the directory that contains it.