fusioncatcher references version

[valleema]

Hello,

I am trying the pipeline and I ran into a little problem that prevents the use of fusioncatcher.

In the script the references are outdated.

So I locally modified it to download the v98 (the currently available one).

However, it does not work when the pipeline is launched.

Maybe due to what is bundled in the singularity image, this is the exit message from Nextflow execution:

  ....................
  ERROR: The version of the data build does not match the version of this pipeline!
  Please, run again the 'fusioncatcher-build.py' in order to fix this!
  ....................

What should I do to resolve it?

[maxulysse]

Hi @valleema I more recently got more involved into this project, and I'm currently focusing on the #54 issue.
I'll look into that first thing after.

[valleema]

Great! And the #54 issue is quite interesting to add, I reckon.

[matq007]

Hey @valleema are you running nf-core/rnafusion:1.0.2? Everything should be compatible

[valleema]

Hi @matq007, yes I am running the "downloaded-yesterday". In the Nextflow code, the download points to a v90 reference, and only the v98 is available.

That's why I manually downloaded the v98, following your help pages.

[matq007]

Ah, I finally see the problem. Damn.. the author removed the old reference. Hmmm... The only option currently that I can think about is to create your own singularity image with the latest fusioncatcher tool.

new environment file

name: fusioncatcher
channels:
  - bioconda
  - conda-forge
dependencies:
  - bioconda::fusioncatcher=1.20

and then cd tools && build.sh fusioncatcher which will generate docker container which can be afterwards transformed into singularity image.

[valleema]

Yes, building my own image was on my mind as well... Tough task, right now as I am not root of any machines around. I might find a way, but it could be a better call to let you time to update the image, for the new users of this pipeline as well.

What do you think?

[valleema]

Or... If you have them somewhere, make the v90 files available to download. It could be a quick solution.

[matq007]

I have fixed the issue on the dev branch. There is a new container on dockerhub which you can download and convert to singularity image. One thing to note is that in order to run fusioncatcher you have to run fusioncatcher.py <commands>.

[valleema]

So, it needs to be 1.20 here :

rnafusion/nextflow.config

Line 14 in 5fea38c

fusioncatcher_version = '1.00'

rnafusion/example/custom-singularity.config

Line 15 in d4a622c

fusioncatcher_version = '1.00'

rnafusion/example/custom-docker.config

Line 15 in d4a622c

fusioncatcher_version = '1.00'

But so far, so good, it runs! Thanks a lot!!!

[matq007]

Ah, thanks for pointing out. We will make these changes once we bump the version

[valleema]

Great. Thanks a lot for your help and your quick solutions!