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jbloomlab / dms_tools2

software for the analysis and visualization of deep mutational scanning data
GNU General Public License v3.0
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Unable to install DMS in conda env or Run Digens 2018 example Notebook #71

Open karenHDT opened 4 months ago

karenHDT commented 4 months ago

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

image

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.

image

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. image

Thank you for your help!

jbloom commented 4 months ago

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 commented 4 months ago

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