diffExp incomplete output

[MustafaElshani]

I have tried to run diffExp with incomplete output, but no errors, I only get the following

dge_stderr.txt  
filtered_gene_counts_ds2.tsv  
filtered_iso_counts_drim.tsv  
filtered_iso_counts_ds2.tsv  
formula_matrix.tsv

I think this problem is the same as reported in #151 #100 #161 #171

From the above issue it seems that rpy2, numpy but then there is conflicts between pandas and numpy and rpy2 and R version.

my current environment includes

python=3.9
rpy2=3.1
numpy=1.19.5
R=4.1.2

[Jeltje]

Hi Mustafa,

Would you mind trying our docker container: docker pull brookslab/flair:latest

You can then run flair commands like so docker run -v `pwd`:/mydata -w /mydata brookslab/flair:latest flair diffExp (...)

(note that you no longer need the .py extension after flair)

If this solves your problem to your satisfaction, please close this ticket.

We're hoping to make the current version of Flair conda installable eventually

[MustafaElshani]

Dear Jeltje

I tried the docker run and diffExp worked properly, it seems to have fixed inconsistencies and all outputs were generated

Thank you, very much appreciated

Mustafa