vSNP3

[vthapanp]

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]

Please send the error message you are receiving.

[vthapanp]

The error I got is following: conda install vsnp -c conda-forge -c bioconda Retrieving notices: ...working... done Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: The following specifications were found to be incompatible with each other: Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system: - feature:/osx-64::__osx==10.16=0 - feature:|@/osx-64::__osx==10.16=0 - vsnp -> matplotlib-base -> __osx[version='>=10.11|>=10.12'] Thanks, Vaskar

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On Wed, Jul 5, 2023 at 12:25 PM stuber ***@***.***> wrote: Please send the error message you are receiving. — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BAQKUBPFXL3C3Q2QEBQFA53XOWIPTANCNFSM6AAAAAAZ7FMWPE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[stuber]

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]

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]

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]

Hi Tod, Thanks for the instructions. Could you provide me the script for how to download fastq files from NCBI to run vSNP. I think that also need to be downloaded to vsnp3_rest_dataset at github.com/USDA-VS for me to run the scripts that you suggested to me. Regards, Vaskar

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On Mon, Nov 27, 2023 at 6:12 AM stuber ***@***.***> wrote: 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. — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BAQKUBL6PVWXZU7TOSOKW5LYGRYTJAVCNFSM6AAAAAAZ7FMWPGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRXGYZDQMZXGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>