Dear IFB-team,
I d like your help with a tool I am trying to install locally. https://rMATS-turbo . It's for alternative Splicing detection.
I ran it by loading python/2.7, (only other option is 3.6).
I also installed in /home/mk/Tools_Packages/gsl-2.6/ the GSL package and configured it because I didn't find any as a module.
If there is a way to call it from existing bin/ in cluster, let me know.
Other dependecies to verify if we have (please let me know how I could see myself in the future) :
Cython (0.29.14)
numpy (1.16.5)
BLAS, LAPACK
GCC (5.4.0)
gfortran (Fortran 77)
CMake (3.15.4)
I get the following error during the ./build_rmats :
rm: cannot remove ‘*.dylib’: No such file or directory make: [build] Error 1 (ignored) cd rMATS_C; make; make[1]: Entering directory "/shared/ifbstor1/home/mkondili/Tools_Packages/rMATS_turbo_4.1.0/rMATS_C" .
some other src/ scripts are runnning , and then .. : /usr/bin/ld: cannot find -lblas /usr/bin/ld: cannot find -llapack collect2: error: ld returned 1 exit status make[1]: *** [rMATSexe] Error 1
Do you have an idea if these errors are due to dependencies or something else wrong during installation ?
Is it possible to install it globally as module if all deps are existing
(at least for some time until I run it) ?
Thanks for the recommendation. This would be fine too.
But how can I run it now ?
I cannot import it as a python package inside python env. (no module named ..!),
and don't know where is the main script saved.
Their tutorial suggests to call it via command-line as : python rmats.py
I need it initially for testing, I found it from a study published, but if it works I could use it on my analysis recurrently.
Well, for the moment I couldn't be very demanding,because I need to run it as soon as possible.
So, if you can install it as a module that would be great.
It was a good practise for me to learn how to install it locally anyway, no problem.
I don't know how "slow" can this one be,compared to turbo, in practice(they say 100x for turbo!). I only have 9 samples to run. I ll use the max of threads possible though.
Would it be too much to ask to update the version of this, because new one is published : 4.1.1 in https://anaconda.org/bioconda/rmats
It gives more verbose msg in errors so it is more useful. You can delete the 4.1.0.