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I'm failing to use this package #2225
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Hello @Hoeze! Thank you for submitting this issue. I assume this is recent, with the most recent release version 0.29.0 of @akmorrow13 Could you also take a look? |
Wow, thanks for the quick reaction 👍 |
I still need to look into this further, which may be difficult as campus is without power at the moment. Meanwhile, one of the following might work Try the most recent development version on PyPI, 0.30.0a0
https://pypi.org/project/bdgenomics.adam/0.30.0a0/ Try installing ADAM via Bioconda
https://bioconda.github.io/recipes/adam/README.html I believe that a link is not created for |
I began installing with EDIT: |
Sorry, I personally don't have that much experience packaging python, and to be honest I get quite confused with regards to conda and pip and virtualenv and such. I created the conda recipe to install the ADAM command line tools I am also not sure I've been thinking it might be worth splitting the R and python libraries into separate repositories, so that they can each have their own language-specific build, release process, and packaging. As it is now, our release script doesn't work all the way through, I have to run the JVM and R parts of it peacemeal, and ask @akmorrow13 to build and deploy the python library (https://github.com/bigdatagenomics/adam/blob/master/scripts/release/release.sh#L60). It might also be worth creating a separate conda recipe that depends on the PyPI package rather than the Maven release distribution tarball, although I don't know what this should be called ( https://bioconda.github.io/contributor/guidelines.html#python |
After a bit of experimenting, removing the egg-related lines from
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Hello @akmorrow13, might you be able to weigh in on this issue? |
@heuermh I am unsure about how/if the pip installations are dealing with the jars, that was setup before my time. I am unsure of whether pip is installing the jars at all? I can update the conda recipe to work more like Mangos, as the conda recipe currently does not install python modules as all. However, I will have to think more about pip. |
Thanks for the quick reply! Before updating the Conda recipe, I would like to try to resolve the problem(s) with the |
Hi all, |
Hello @alartin, unfortunately I am not much more informed on python packaging than in 2019 😉 If you have a workaround that works for you, keep going with it! I'm typically using the adam python libraries from a jupyter or quarto notebook and thus don't use the |
Hi, I try to install this package and use it but I'm constantly failing.
What I did so far:
pip install bdgenomics.adam
pyadam
When I try to use the Python API I get the following result:
The text was updated successfully, but these errors were encountered: