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rrwick / Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes
GNU General Public License v3.0
306 stars 28 forks source link

Problem with mamba/conda install #13

Closed clf-bio closed 3 years ago

clf-bio commented 3 years ago

I got the following error when I tried to install Trycycler with mamba (another anaconda package mangaer):

`I got the following error when I tried to install Trycycler with mamba (another anaconda package mangaer):

Looking for: ['trycycler']

bioconda/linux-64 [====================] (00m:00s) No change bioconda/noarch [====================] (00m:00s) No change anaconda/pkgs/main/linux [====================] (00m:00s) No change anaconda/pkgs/r/linux-64 [====================] (00m:00s) No change anaconda/pkgs/main/noarc [====================] (00m:00s) No change anaconda/pkgs/r/noarch [====================] (00m:00s) No change anaconda/pkgs/msys2/linu [====================] (00m:00s) No change anaconda/pkgs/msys2/noar [====================] (00m:00s) No change Encountered problems while solving. Problem: nothing provides icu 54.* needed by r-base-3.4.1-0`

And I got the following error when I tried to install Trycycler with conda: `Found conflicts! Looking for incompatible packages. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions`

rrwick commented 3 years ago

I'm no expert with conda stuff, but I've done some experimenting and I may have found a solution.

I managed to reproduce your issue (or at least something very similar) on Ubuntu 18.04. I narrowed the problem to the r-phangorn package, which is one of the dependencies in the Trycycler conda recipe. I then found this issue which highlighted the problem: I didn't have the conda-forge channel set up, which is a requirement for Bioconda.

Once I fixed that (conda config --add channels conda-forge) I was able to successfully run conda install trycycler. And I've taken what I've learned in this process and updated the Software requirements and Installation pages of the wiki.

I hope that fixes the issue for you too! If not, let me know.

Ryan

clf-bio commented 3 years ago

Maybe my issue was caused by the anaconda mirror ( I'm using a conda mirror to speed up downloading process). I solved this problem by switching back to the official conda channel (with bioconda & conda-forge channel configured)

rrwick commented 3 years ago

Glad to hear you got it working!