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DessimozLab / read2tree

a tool for inferring species tree from sequencing reads
MIT License
138 stars 18 forks source link

Installation issue using conda #39

Closed InfiniteLaugh closed 10 months ago

InfiniteLaugh commented 10 months ago

Dear developers,

Thanks first for developing this interesting software which gives me another aspect to deal with my work.

I try to use more than 3000+ samples, with genome size at around 400M, to construct a phylogenetic tree, and I hope to use this software to make it without calling SNP (This might take a very long time).

However, When running the following: conda create -n r2t python=3.10.8 conda install -c bioconda read2tree

I get this output and error:

` Collecting package metadata (current_repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source. Collecting package metadata (repodata.json): done Solving environment: unsuccessful initial attempt using 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:

Your installed version is: 2.31 `

As I shown above, I built a new environment with python-3.10.8. My conda version is 23.7.2.

I am not the administrator, so I can't install this software with Docker or something else.

Could you please give me some advice?

Yours sincerely, Jethro

sinamajidian commented 10 months ago

Hi Thanks for using read2tree. You could try using mamba as discussed here or installing from source described here. Please let us know if more details is needed.

‌Best regards, Sina

InfiniteLaugh commented 10 months ago

Hi Thanks for using read2tree. You could try using mamba as discussed here or installing from source described here. Please let us know if more details are needed.

‌Best regards, Sina

Hi @sinamajidian

Thank you for getting back to me so quickly.

I have re-installed the software with mamba and it seems to works out well.

Thank you again for your help!