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Clinical-Genomics / fusion-report

Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/

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Tiny code issue with latest update

Rmulet opened this issue · comments

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Hi,

First of all, thanks a lot for this great tool! It's a great idea :)

However, the latest version available on this repository doesn't work out of the box for me. I had to make a minor modification in the code of fusion_manager.py, which was changed upon merger of the latest pull request. The set_header() function was missing the argument it expects, so I added line as a quick fix:

                    line: str = fusion_output.readline().replace('"', '').strip()
                    factory_parser.set_header(line)

I have also had other issues with the installation, but I could fix them by modifying the requirements.txt file. Namely, newer versions of markupsafe don't have the name soft_unicode, which breaks jinja2 (explained here: aws/aws-sam-cli#3661). Besides, the installation of python-rapidjson 0.70 fails with python 3.10.

The version of fusion-report available on conda works just fine (with none of the issues I just mentioned), but I wanted to use jaffa, which is only available in 2.1.5.