ERROR: trimmomatic is not installed.

[viromelab]

ERROR: trimmomatic is not installed.

[pratas]

Hi,
what happens if you run:
trimmomatic -version

[leesaudan2]

$ trimmomatic -version
bash: trimmomatic: command not found

[pratas]

It seems that trimmomatic is not installed.
Lets find out why. Please, run this:

conda install -c bioconda trimmomatic --yes

(it will try to install trimmomatic)

[leesaudan2]

Then, how come:

$ conda list | grep trim
trimmomatic               0.39                 hdfd78af_2    bioconda
$ conda run trimmomatic -version
0.39

???

[leesaudan2]

And more:

$ conda install -c bioconda trimmomatic --yes
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

$ conda run trimmomatic -version
0.39

Not installed???

[leesaudan2]

After

conda install -c bioconda trimmomatic --yes

I still get the same error message when running

./TRACESPipe.sh --install

☹️

[pratas]

Sorry, it is installed, but it seems that you don't have full access to the machine.
Your conda seems to be installed through a virtual interpreter.
Which operating systems are you using? Is it a virtual one?

[pratas]

This is a conda issue not from TRACESPipe.
Once fixed, after running

./TRACESPipe.sh --install

if you run

trimmomatic -version

you have to get the same output, which is

0.39

TRACESPipe assumes that the binaries for each tool (under conda) are directly accessible.

[leesaudan2]

No. I'm not using any virtual interpreter.

I installed conda by following these instructions. This is on Linux (Debian bullseye/sid) on a real machine (x86_64).

[leesaudan2]

What do you mean by "full access"? Root privilege? It can't be installed as a normal user?

[pratas]

It can. I've tried in a new machine and it works fine.
Not sure why it doesn't on yours...

[pratas]

Can you generate a virtual linux (ubuntu) and test again?

[pratas]

Maybe the OS runs through the interpreter and does not add the binaries directly

[pratas]

For example if I do

locate trimmomatic

I get

/home/(user)/miniconda3/share/trimmomatic

or

home/(user)/miniconda3/bin/trimmomatic

[pratas]

Please check you .bashrc

a see if there is something like:

__conda_setup="$(CONDA_REPORT_ERRORS=false '/home/(user)/miniconda3/bin/conda' shell.bash hook 2> /dev/null)" if [ $? -eq 0 ]; then \eval "$__conda_setup" else if [ -f "/home/(user)/miniconda3/etc/profile.d/conda.sh" ]; then . "/home/(user)/miniconda3/etc/profile.d/conda.sh" CONDA_CHANGEPS1=false conda activate base else \export PATH="/home/(user)/miniconda3/bin:$PATH" fi fi unset __conda_setup

[leesaudan2]

Yes, my .bashrc contains something similar. However, it only adds ".../miniconda3/condabin" to my $PATH. It doesn't add ".../miniconda3/bin" to my $PATH.

Adding ".../miniconda3/bin" manually to $PATH makes it work. I'm still puzzled why those lines added to .bashrc by conda init do not add that to $PATH. It should be a conda problem, then.

Thanks.