Question: Bash: salmon command not found
gravatar for ab123
11 days 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 • 127 views
ADD COMMENTlink written 11 days ago by ab12340
gravatar for ATpoint
11 days ago by
ATpoint9.3k 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 11 days ago by ATpoint9.3k

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 11 days ago by ab12340

Can you link that script?

ADD REPLYlink written 11 days ago by ATpoint9.3k

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

ADD REPLYlink written 11 days ago by WouterDeCoster34k
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