Closed leesaudan2 closed 3 years ago
Hi, what happens if you run: trimmomatic -version
$ trimmomatic -version
bash: trimmomatic: command not found
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)
Then, how come:
$ conda list | grep trim
trimmomatic 0.39 hdfd78af_2 bioconda
$ conda run trimmomatic -version
0.39
???
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???
After
conda install -c bioconda trimmomatic --yes
I still get the same error message when running
./TRACESPipe.sh --install
:frowning_face:
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?
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.
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).
What do you mean by "full access"? Root privilege? It can't be installed as a normal user?
It can. I've tried in a new machine and it works fine. Not sure why it doesn't on yours...
Can you generate a virtual linux (ubuntu) and test again?
Maybe the OS runs through the interpreter and does not add the binaries directly
For example if I do
locate trimmomatic
I get
/home/(user)/miniconda3/share/trimmomatic
or
home/(user)/miniconda3/bin/trimmomatic
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
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.
I have the same problem,but I still don't know how to issue it ,so I want to konw the solution,please.
I was following the installation instructions.
When I run
I get this error:
But trimmomatic has been installed in the conda environment:
What's wrong?
I'm using version d685d0cf82db6da631a11e2c9c2338c847418d19.