Open tohsumi-bebio opened 1 year ago
Thanks @tohsumi-bebio I just created a PR with a new environment that solves this issues. I tested it on several machines and the tests all passed. Let me know if you still have any issues.
Dear Dr. Rubio,
Thank you very much. How can I retrieve the updated code? I just tried to clone the repository, https://github.com/editasmedicine/uditas.git, but still getting errors on Debian. Many thanks,
Toshi
Dear @tohsumi-bebio , the PR has been merged and you can pull the new code. Only the yaml file to create the conda environment has changed.
Let me know if you have any issues.
I am having the same error as tohsumi-bebio. I have made a conda environment from the current 'uditas_env.yml' file but the tests 2a and 2b fail. Can be this a problem outside of the scope of the environment? I welcome any suggestions how to fix it.
=========================== short test summary info ============================
FAILED test/test_fig2a.py::test_fig2a - assert 0.0031203054434319477 < 1e-05
FAILED test/test_fig2b.py::test_fig2b - assert 0.003202984373900788 < 1e-05
=================== 2 failed, 1 passed in 412.10s (0:06:52) ====================
Greetings,
I am interested in running the UDiTaS pipeline. I notice that Bio.Alphabet is removed from Biopython since version 1.78. Your code uses it in uditas/uditas_helpers.py, IUPAC.unambiguous_data. Thus, I added =1.77after the biopython entry in uditas_env.yml. After creating the environment and setting the environment variables BOWTIE2_INDEXES and GENOMES_2BIT, I ran pytest, but got the below output and error. Might you know what may be going on here? I imagine that the output is not what is to be expected. Many thanks,