Question: Bash: salmon command not found
gravatar for ab123
7 months ago by
ab12340 wrote:

Hello there,

Has anyone gotten Salmon to work in Terminal?

It keeps telling me that the command does not exist.

I've already upgraded Anaconda and ran the command as just "activate salmon" instead of "conda activate salmon". The file has also been removed from the bash_profile as recommended in the salmon notes.

Any tips?


Output when running conda activate salmon below (as mentioned I ran the suggestions):

conda activate salmon

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If your shell is Bash or a Bourne variant, enable conda for the current user with

    $ echo ". /anaconda3/etc/profile.d/" >> ~/.bash_profile

or, for all users, enable conda with

    $ sudo ln -s /anaconda3/etc/profile.d/ /etc/profile.d/

The options above will permanently enable the 'conda' command, but they do NOT
put conda's base (root) environment on PATH.  To do so, run

    $ conda activate

in your terminal, or to put the base environment on PATH permanently, run

    $ echo "conda activate" >> ~/.bash_profile

Previous to conda 4.4, the recommended way to activate conda was to modify PATH in
your ~/.bash_profile file.  You should manually remove the line that looks like

    export PATH="/anaconda3/bin:$PATH"

^^^ The above line should NO LONGER be in your ~/.bash_profile file! ^^^
bash rna-seq salmon • 555 views
ADD COMMENTlink written 7 months ago by ab12340
gravatar for ATpoint
7 months ago by
ATpoint18k wrote:

None of these errors have anything to do with salmon. What you apparently did was to create a new environment termed Salmon. Did you install Salmon itself: conda install -c bioconda salmon?

ADD COMMENTlink written 7 months ago by ATpoint18k

Hi there, thanks for the answer. I followed the Salmon user script which doesn't mention the install command. I ran install and that seems to have solved the problem! Thank you!

ADD REPLYlink written 7 months ago by ab12340

Can you link that script?

ADD REPLYlink written 7 months ago by ATpoint18k

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

ADD REPLYlink written 7 months ago by WouterDeCoster39k

Any such package can be installed with the general command

conda install -c bioconda package

but for some packages from repositories for Bioconductor package you have to link it to the uploader such as

conda install -c bioconda bioconductor-shortread

One easy way is to google 'conda salmon' and then follow the link on Anaconda website which has instructions to install it on Linux using the above commands.


ADD REPLYlink written 5 months ago by devbt1510
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