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Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
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Installing Cyrius using pip for ease of use with other python tools #39

Open timsanford opened 11 months ago

timsanford commented 11 months ago

Hello,

I ran "!pip install git+https://github.com/Illumina/Cyrius.git" in a cell in my jupyter notebook and received the following output:

Collecting git+https://github.com/Illumina/Cyrius.git Cloning https://github.com/Illumina/Cyrius.git to /tmp/pip-req-build-atgcxnnp Running command git clone --filter=blob:none --quiet https://github.com/Illumina/Cyrius.git /tmp/pip-req-build-atgcxnnp Resolved https://github.com/Illumina/Cyrius.git to commit 9fb1c6d0858526463922fd114a3513c3bfaefc29 ERROR: git+https://github.com/Illumina/Cyrius.git does not appear to be a Python project: neither 'setup.py' nor 'pyproject.toml' found.

Is there any way that i can install and import Cyrius so that it can be used in my workflow more efficiently? I am working in a cloud-based environment within a research project's platform. Let me know if there is a possible solution. Thank you for your help!

timsanford commented 11 months ago

Hi, just to update I also tried using conda as shown below and got the following message:

!conda install -c https://github.com/Illumina/Cyrius.git Cyrius

Collecting package metadata (current_repodata.json): failed NotWritableError: The current user does not have write permissions to a required path. path: /opt/conda/pkgs/cache/69d154c7.json uid: 1000 gid: 100 If you feel that permissions on this path are set incorrectly, you can manually change them by executing $ sudo chown 1000:100 /opt/conda/pkgs/cache/69d154c7.json In general, it's not advisable to use 'sudo conda'.

Any suggestions on installing Cyrius tools? Thank you for the help.

xiao-chen-xc commented 11 months ago

Hi @timsanford, you can now find Cyrius on pip. pip install cyrius And it can be run with the command cyrius -h. The parameters are the same as listed in README.

timsanford commented 7 months ago

Thank you for your help. In order to run our analysis, we need to run a dsub job that uses cyrius. Do you know of any docker images that have cyrius pre-installed in order to use them for the dsub job? We are not able to run pip within the environment we are using, so have to proceed this way. Thanks again.