Closed amizeranschi closed 4 years ago
Hi,
Ragout could not find the binary files - something must be wrong with the bioconda environment. If you installed Ragout into a separate environment, make sure it is activated. Your bin folder can't be the one from your new environment, since there are so many unrelated binaries.
I suggest to create a new clean Py2.7 environment: conda create -n py27 python=2.7
, then do conda activate py27
and then conda install ragout
. You can then verify if the binaries are installed by using which ragout-maf2synteny
.
Mikhail
Hi Mikhail,
Thanks for the reply. This was a problem with my PATH setup (I had a typo).
I have Ragout installed in a conda environment and cactus (with Hal) in a separate one.
After fixing the PATH and setting up PYTHONPATH to point to the right locations from the conda environments:
export PYTHONPATH=/export/home/ncit/external/a.mizeranschi/ragout_conda/anaconda/lib/python2.7/site-packages:/export/home/ncit/external/a.mizeranschi/cactus_conda/anaconda/lib/python2.7/site-packages:$PYTHONPATH
Ragout now works fine for me.
Hi,
I've installed Ragout from Bioconda into a new environment (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/ragout/meta.yaml)
and I'm getting an error while running Ragout on Cactus's
evolverMammals
example (https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/master/examples/evolverMammals.txt):Does anyone have a clue about what I'm doing wrong here? Or is it just a problem with the Bioconda recipe? The
maf2synteny
executable does indeed seem to be missing from my system.This is what the bin directory looks like: