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.
@gildaslecorguille Bonjour, désolé de réouvrir ce sujet
Depuis la semaine passée j'utilise le module rMATS et jusqu'à jeudi dernier il fonctionnait bien mais maintenant je recoit cette erreur:
Command error:
Traceback (most recent call last):
File "/shared/ifbstor1/software/miniconda/envs/rmats-4.1.1/bin/rmats.py", line 19, in <module>
from rmatspipeline import run_pipe
ModuleNotFoundError: No module named 'rmatspipeline'
Elle est associée à cette issue mais comme je ne l'ai pas moi même installé, je ne sais quoi faire
Oui il fonctionnait toujours pour moi ainsi mais dans un processus nextflow, sans explications il a arrêté de fonctionner, chaque fois j'obtenais l'erreur qie je vous ai envoyée plus haut.
Actuellement pour faire fonctionner ce worflow, j'utilise une image docker avec singularity.
Ça pourrait être le cas mais il fonctionnait avant sans problèmes, je n'y ai fait aucune modifications et du jour au lendemain il a arrêté de fonctionner
Bonjour,
J'ai le même problème...
Je suis dans un directoire avec mes fichiers bam et un fichier.txt de groupement des bam. Lorsque je fais
module load rmats/4.1.1
Puis
python rmats.py --b1 g1_file.txt --b2 g2_file.txt --gtf path/to/gtf -t single --readLength 75 --variable-read-length --nthread 4 --od rmats_res --tmp rmats_res
J'obtiens alors l'erreur
python: can't open file 'rmats.py': [Errno 2] No such file or directory
Si je télécharge le fichier rmats.py à partir de l'archive de rmats/4.1.1 et que j'exécute la même commande, j'obtiens :
Traceback (most recent call last):
File "rmats.py", line 19, in
from rmatspipeline import run_pipe
ModuleNotFoundError: No module named 'rmatspipeline'
ajouter le "path" de rmats avant le script '.py' parce que le package n' est pas installé dans ton "home" mais dans le dossier des packages de ifb , càd :
