settings.txt does not exist

[royfrancis]

Hi, I get the following error when I run MISO.

Error: Settings file /home/rmf/.pyenv/versions/2.7.6/lib/python2.7/site-packages/misopy/settings/miso_settings.txt does not exist.

I am running my code like so:

miso \
--run="$path/miso-index/" \
--read-len=126 \
--use-cluster \
--paired-end=PAIRED_END \
--output-dir="something-miso" \
--prefilter \
something.bam

I think my python environment is ok.

matplotlib==2.0.2
misopy==0.5.4
numpy==1.13.1
pandas==0.19.2

samtools and bedtools are loaded as well.

I was wondering if you might have any ideas on what might be wrong.

[sepidehparhami]

I ran into this problem too; a quick fix is to copy over the miso_settings.txt from this repo into ./misopy/settings on your computer

[yarden]

This is an indication that the package was not installed correctly; settings.txt should be available as data from the installed package directory. Did you install with a package manager like pip?

[royfrancis]

Yes. It was installed using pip. I am using python using pyenv on a cluster. It was complaining this does not exist /home/rmf/.pyenv/versions/2.7.6/lib/python2.7/site-packages/misopy/settings/miso_settings.txt. So I checked at this location and the miso_settings.txt and the settings directory was missing. I created the directory and copied it from this website as suggested by @sepidehparhami.

Now, it complains about output folder although it has been provided (as shown in my first comment). Error: need --output-dir to compute Psi values.

[chonga2022]

did you solve this error？

[chonga2022]

I got the same error