failing to install rMATS

Question

[thomas.heigl.ibk]

Hey Biostar Community.

Recently, I started diving into alternative splicing projects and tested DEXSeq, which works for me. A different approach would be to use rMATS, I thought, however, not an easy one as I fail to install this tool.

I ran from one error into the next and now I don't know how to proceed.

What I did was to setup an environment with conda and install the dependencies with a yml file:

name: rmats
channels:
  - conda-forge
  - defaults
dependencies:
  - python=3.6.12
  - cython=0.29.21
  - blas
  - lapack
  - gsl=2.5
  - gcc_linux-64>=5.4.0
  - gfortran_linux-64
  - cmake=3.15.4
  - samtools   
  - star       
  - pairadise 

Thereafter, I tried to build rMATS and ran into some errors, for which I needed to install other things (cannot remember anymore what exactly). And now, I got stuck.

When I build_rmats it stops at following step:

...
cd rMATS_pipeline; python setup.py build_ext;
running build_ext
cp `find ./rMATS_pipeline/build | grep so` .;
Cloning into 'PAIRADISE'...
remote: Enumerating objects: 137, done.
remote: Counting objects: 100% (83/83), done.
remote: Compressing objects: 100% (67/67), done.
fatal: the remote end hung up unexpectedlyB | 114.00 KiB/s 
fatal: early EOF
fatal: index-pack failed
(rmats) 

I repeated with new environments. Tried different approaches but somehow I always end up at this step failing.

Any suggestions? And also any suggestions what to use instead of rMATS that could be used purely inside of R, as I do alignment and counting with Rsburead and featurecounts.

[truong128]

Hello Biostar Community,

I use MacOS and I'd like to install rMATs into my Mac. I tried to install it several times and failed!!! Could you please help if you could install rMATs on Mac? Many thanks

Ryan

Answer 1

[kutscherae]

rMATS is available as a bioconda package which might work for you:

conda install -c conda-forge -c bioconda rmats=4.2.0

From this post it seems like maybe the error is from git: https://stackoverflow.com/questions/21277806/fatal-early-eof-fatal-index-pack-failed

And it looks like it's happening at this part of the rMATS build where it tries to install PAIRADISE from github: https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/build_rmats#L77

PAIRADISE is only used if rMATS is run with --paired-stats. You can tell the build to skip pairadise with: ./build_rmats --no-paired-model

If you do want to use --paired-stats then you could try creating a new conda environment with these dependencies and then running ./build_rmats. Potentially you'll need to set some envionrment variables as well:

CPATH to avoid an error about zlib.h and FC to avoid an error about f77

requirements.txt:

Cython=3.0.*
cmake=3.27.*
gcc=13.*
gfortran=13.*
gsl=2.7
gxx=13.*
liblapack=3.9.*
python=3.10.*
r-base=4.3.*
r-doparallel=1.0.*
r-foreach=1.5.*
r-iterators=1.0.*
r-nloptr=2.0.*
zlib=1.2.*

conda create --prefix ./rmats_conda_env
conda activate ./rmats_conda_env
conda install -c conda-forge -c bioconda --file requirements.txt
export CPATH="${CPATH}:/path/to/rmats_conda_env/include"
export FC="$(which gfortran)"
./build_rmats

[thomas.heigl.ibk]

thanks a lot.

downloading it from bioconda worked for me. I guess all the other part belong to rMATS such as producing sashimi plots are also found there.