martynaut/mirnome-mutations

Version for Windows

Opened this issue · 3 comments

telumar commented

Is it possible to use the miRMut pipeline on Windows?

martynaut commented

Currently we are not supporting Windows due to the hgvs library usage, however we plan to resolve it in the future. We strongly encourage our users to use the mirnome-mutations scripts on unix systems.

However, if someone for some reason cannot use unix system, insists on using Windows and accepts that not all of the functionalities (genomic and transcriptomic hgvs) will be available, please follow instructions below.

  1. Before installing dependencies from requirements.txt file remove the "hgvs" line from the requirements.txt file
  2. Comment or remove line 8 ("from add_hgvs_nomenclature import hgvs_nomenclature, hgvs_n_nomenclature") in run_mirnaome_analysis.py file
  3. Comment or remove lines 81 and 82 ("hgvs_nomenclature(output_folder)", "hgvs_n_nomenclature(output_folder)") in run_mirnaome_analysis.py file
  4. Change "/all_mutations_with_n_hgvs.csv" to "/all_mutations_with_weights.csv" in line 13 of distinct_occure.py file

The steps need to be done only once and after that the analyses may be run as in unix examples.

Please let me know if you have any other questions.

  • 👍1
martynaut commented

I will keep this issue open to increase viewability of the answer.

telumar commented

Thank you Martyna