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vSNP3 #3

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vthapanp opened this issue Jul 5, 2023 · 6 comments
Open

vSNP3 #3

vthapanp opened this issue Jul 5, 2023 · 6 comments

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@vthapanp
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vthapanp commented Jul 5, 2023

I tried to download vSNP3 in MacOS Monterey, ver 12.6.7 and it does not work. Do you have any suggestions? I followed the installation instructions that are provided for Mac users. Thanks!

@stuber
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stuber commented Jul 5, 2023

Please send the error message you are receiving.

@vthapanp
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vthapanp commented Jul 5, 2023 via email

@stuber
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stuber commented Jul 6, 2023

Thank you for providing the error. Since the error is originating from the conda install finding incompatible specifications, possibly vsnp3 is being installed in base or in another environment that is causing conflicts. Please try the following and let me know if this helps. Below will install vsnp3 in a new environment which should avoid conflicts.

  1. If in a current environment deactivate. This will put you in "base".

    conda deactivate
    
  2. Create a new environment called "vsnp3":

    conda create --name vsnp3
    
  3. Activate the newly created "vsnp3" environment:

    conda activate vsnp3
    
  4. Install vsnp3 version 3.14 from the conda-forge and bioconda channels:

    conda install vsnp3=3.14 -c conda-forge -c bioconda
    

Additionally, you may find this link helpful. This is my go-to for managing environments.

@vthapanp
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Hi,

What script to use to download fasta sequences saved in a computer and then run step 1 and step 2 for vsnp3.14

@stuber
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stuber commented Nov 27, 2023

Follow the steps here if using vSNP3 to analyze TB, Brucella or SARS-CoV-2, https://github.com/USDA-VS/vSNP3#test-workflow. The 3 steps will be:

cd ~; git clone https://github.com/USDA-VS/vsnp3_test_dataset.git
cd ~/vsnp3_test_dataset/vsnp_dependencies
vsnp3_path_adder.py -d `pwd`

After running vsnp3_path_adder.py the reference types will be ready to use. After running the above the reference types available can be seen using, vsnp3_path_adder.py -s.

If making a new reference type let me know and I can provide more detail.

@vthapanp
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vthapanp commented Nov 27, 2023 via email

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