Unable to install DMS in conda env or Run Digens 2018 example Notebook

[karenHDT]

Dear dms_tools2 authors,

I am having trouble intalling dms_tools2. After reading previous issue threads I tried creating a conda virtual environment.

1. install conda, update conda
2. intialize conda
3. create a conda environment with python 3.11.5, named DMS021324
4. tried to install dms_tools2

• PackagesNotFoundError: The following packages are not available from current channels: dms_tools2

6. install git and pip
7. install dms_tools with pip install git+git://github.com/jbloomlab/dms_tools2.git

In addition, I have tried running the Digens 2018 example analysis notebook. Import dms_tools2 failed in the first code block because of missing packages. I ran !pip install dms_tools2, however I ran in to a similar issue.

I would love to solve this so I can run the python notebook and use this package for my own data.

If a solution is difficult to find - could I possibly request a exported conda environment to import in to my VS code? I see that in Anavonda Navigator I can import conda environements from my local drive.

Thank you for your help!

[jbloom]

Unfortunately we do not have a conda environment with dms_tools2 (so far as I know), and just typicall install with pip.

@ckikawa, do you have any suggestions as you may have been most recent one to use this?

[ckikawa]

This is an environment YAML that I've used as recently as ~3 months ago. I pinned a lot of these packages a few years ago and haven't had issues since.

name: zikv_dmstools2
channels:
  - bioconda
  - r
  - conda-forge
  - defaults
  - schrodinger
dependencies:
  - imagemagick
  - jupyterlab
  - mamba
  - nbdime
  - nodejs
  - pandas=0.25.3
  - pip
  - python=3.8
  - pip:
    - dms_tools2==2.6.10
    - dmslogo==0.6.2
    - snakemake==6.5.2
    - altair
    - vega_datasets
    - dms_variants
    - scipy==1.6.0
    - numpy==1.19.5