I am trying to install rmats using conda install -c bioconda rmats and I keep getting this issue
**UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- rmats -> python[version='2.7.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
Your python: python=3.8
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.**
I have tried changing my python version to 3.7.0 by creating a virtual conda environment, but I got the same issue. Any suggestions?
@ATpoint - Unfortunately the versions reported on the bioconda frontpages are unreliable (see also this issue). In fact, at the time of this writing the meta.yaml file of rmats doesn't impose any restriction on the python version.
Do you run on Mac? I tried to do the build step and got this error:
rm: .so: No such file or directory rm: *.so.: No such file or directory cd rMATS_C; make; cd lbfgs_scipy && make gfortran -c -O2 -c
-o lbfgsb.o lbfgsb.f gfortran -c -O2 -c -o linpack.o linpack.f gfortran -c -O2 -c -o timer.o timer.f
Traceback (most recent call last):
File "/Users/heltonn/rmats/rmats-turbo/rmats.py", line 16, in <module>
from rmatspipeline import run_pipe
ModuleNotFoundError: No module named 'rmatspipeline'
If your conda is not working specifically for rmats. You could try alternatively creating a Python 3.6 or Python 2.7 environment with conda and then downloading the pre-built package (for your respective python version) from the rmats maintainer:
If I read this correctly it needs python2.
@ATpoint - Unfortunately the versions reported on the bioconda frontpages are unreliable (see also this issue). In fact, at the time of this writing the meta.yaml file of rmats doesn't impose any restriction on the python version.
As of the newest release: http://rnaseq-mats.sourceforge.net/
It is now:
As a side note, I'm successfully running rmats v4.1.0 with python v3.6.5 installed through conda in August
Do you run on Mac? I tried to do the build step and got this error:
and if I try to ./run_rmats I get this error:
Not quite sure of the issue.
Is this after installing it with conda or downloading the "pre-compiled" version?
I've tried both ways and get the same results.
Make a separate environment and install rmats in it. Avoiding these conflicts by making separate environments is the whole point of using conda.