suhrig/arriba

Conda recipe

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matq007 commented

Would it be possible to wrap the tool into conda package and upload it to bioconda? I am working on a rnafusion pipeline which consists of multiple tools for fusion detection. It would be super nice to implement your tool to the stack 🎉

suhrig commented

Hi Martin,

After someone made me aware of your project yesterday, I was going to get in touch with you anyway to discuss the possibility/technical details of integrating Arriba into your pipeline. You found me faster. :-)

Sure, I can prepare a bioconda package. If it suits your time frame, I will distribute it with the next stable release of Arriba, which I plan to release in a few weeks. I'll keep you updated.

Arriba's workflow is very similar to that of STAR-Fusion. I imagine we can make use of a lot of copy-pasta, which should facilitate the integration.

Regards,
Sebastian

  • 👍2
matq007 commented

Hi Sebastian, that sounds perfect. I am working on few changes now anyway so just let me know when you are ready 👍. I would like to include the tool in version 1.2 which will be maybe in a month or 2.
Look forward 🎉

Martin

suhrig commented

I managed to port the current version of Arriba (1.0.1) to bioconda. You should now be able to install it. Version 1.1.0 is coming soon.

Three executables are installed:

  • arriba (the core executable)
  • run_arriba.sh (a simplistic script to run Arriba starting with FastQ files)
  • draw_fusions.R (an R script to generate figures from the fusion predictions)

In addition, database files (blacklists, protein domains, cytobands, ...) are installed to $CONDA_PREFIX/var/lib/arriba/. You can find more information about all of these in the manual. You can let the content of run_arriba.sh be a guide to you on how to call the tool and integrate it into your pipeline. Let me know, if you need help.

matq007 commented

That sounds perfect. I will probably wait for the 1.1.0 version so I can finish the report in the meantime. I've decided to have a separate repository for the report tool together with a scoring function of the fusions. You can see it here. Look forward to implement the tool to the stack 👍

suhrig commented

FYI: Version 1.1.0 is out, along with instructions on how to install it using Bioconda: https://arriba.readthedocs.io/en/latest/quickstart/#installation-using-bioconda

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xiucz commented

/+ 1 good job.

matq007 commented

Hey @suhrig and @xiucz. I am trying to install arriba with conda but I always get stuck on Solving environment: ...working.... Have you encountered similar issues?

suhrig commented

I just tried it with the most recent Miniconda and it worked right away. But I can confirm this issue in general with conda. I have seen this with a number of packages. sigh

One of these might help:

  • explicitly specify the version of Arriba you want to install (conda install ... arriba=1.1.0)
  • only use the required channels and skip all other activated channels (conda install --override-channels -c conda-forge -c bioconda -c defaults arriba=1.1.0)
  • update conda to the latest version
matq007 commented

Thanks, finally managed to install it. I had a wrong order of the channels.