Question: update salmon with conda
0
gravatar for eridanus
3 days ago by
eridanus0
eridanus0 wrote:

I have installed Salmon with conda. However, I think that an old version has been installed (I get some errors). How could I update with conda? I have tried conda update salmon but nothing happened. I could not install manually that s the reason I used conda. Any solutions? Thank you!

rna-seq • 74 views
ADD COMMENTlink modified 3 days ago by dariober11k • written 3 days ago by eridanus0
2
gravatar for Devon Ryan
3 days ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

Make sure conda-forge and bioconda are in your channels: conda install -c conda-forge -c bioconda salmon=1.3.0. I assume you're not running this on Windows, since we (Bioconda) only ship for Linux and OSX at the moment.

ADD COMMENTlink written 3 days ago by Devon Ryan97k
1
gravatar for Rob
3 days ago by
Rob4.5k
United States
Rob4.5k wrote:

Have you tried conda install salmon=1.3.0, to specifically request the latest version? Sometimes, there are strange package conflicts, and so the other thing you can try is to create a new, blank, environment, and install salmon there.

ADD COMMENTlink written 3 days ago by Rob4.5k

thank you for your answer! I tried your suggestion and it says PackagesNotFoundError..hmm maybe should I try docker..?

ADD REPLYlink written 3 days ago by eridanus0
2

Let me tag @Devon Ryan here as well, since he may have an idea what's going on with bioconda.

ADD REPLYlink written 3 days ago by Rob4.5k
0
gravatar for dariober
3 days ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

PackagesNotFoundError: Do you have the bioconda channel available? You can check with:

conda config --show channels

Which should print something like:

channels:
  - conda-forge
  - bioconda
  - defaults

If you don't see bioconda there, check the installation instructions to fix it.

Also, I would suggest switching to mamba for installing packages (consider that snakemake recommends installing with mamba so it should be pretty reliable)

ADD COMMENTlink written 3 days ago by dariober11k
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