doctor.py error "/usr/bin/env: 'python': No such file or directory", and "-bash: syntax error near unexpected token '('" when activating bioinfo

[TongWu06]

Description of the problem
After installing Biostar Handbook software using the provided installation script, I encountered two issues:

When running micromamba activate bioinfo, I see the message -bash: syntax error near unexpected token '('. However, the prompt does change to (bioinfo), so it seems partially activated.
When running doctor.py inside the environment, I get the error: /usr/bin/env: 'python': No such file or directory.
Steps to reproduce
Commands I executed and their outputs:

> wutong@LAPTOP-TKU3BFJH:~$ curl http://data.biostarhandbook.com/install.sh | bash 
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
>                                  Dload  Upload   Total   Spent    Left  Speed
> 100  4503  100  4503    0     0    580      0  0:00:07  0:00:07 --:--:--  1200
> #
> # Welcome to the Biostar Handbook!
> #
> # Web: https://www.biostarhandbook.com/
> #
> # Setting up bioinformatics tools.
> #
> # 1. Installing micromamba
> #
> # 2. Configuring micromamba channels
> #
> # 3. Configuring the shell
> #
> Running `shell init`, which:
> # 4. Creating the bioinfo environment
> #
> # 5. Installing tools into bioinfo
> #
> # 6. Installing doctor.py
> #
> # 7. Installing the bio package
> #
> # 8. Installing Entrez Direct
> #
> # 9. Installing the SRA toolkit
> #
> # The Biostar Handbook software installation has completed!
> #
> # Restart the terminal or type: source ~/.bash_profile
> #
> wutong@LAPTOP-TKU3BFJH:~$ source ~/.bash_profile
> 
> wutong@LAPTOP-TKU3BFJH ~
> $ micromamba activate bioinfo
> -bash: syntax error near unexpected token `('
> (bioinfo)
> wutong@LAPTOP-TKU3BFJH ~
> $ doctor.py
> /usr/bin/env: 'python': No such file or directory
> (bioinfo)

Expected behavior
Activating the environment should not trigger a bash syntax error.
Running doctor.py inside the bioinfo environment should work normally and detect the Python interpreter.

Actual behavior
Bash shows -bash: syntax error near unexpected token '('.
Running doctor.py fails with /usr/bin/env: 'python': No such file or directory.

Thanks in advance!

[ialbert]

this is a curious error, something must have gone wrong along the way

can you email me the .bash_profile file (don't attach it here since you might have information in there that should not be public)

[TongWu06]

Thank you for your reply! I have already sent the relevant email to your Gmail

[ialbert]

the two files you sent work fine, alas there are many files that are read upon startup

check the following and let me know which file fails:

source .profile
source .bash_profile
source .bashrc
source .biostar.sh 

send me all the files in fact, what I currently have are .profile and .bashrc

[ialbert]

Also, what operating system are you using? I have used the installation instructions on a Mac to reinstall software, and it completed as expected.

[ialbert]

In a nutshell, it seems that the bash startup script has an invalid syntax in it for some reason - it is not clear what has caused it, but evidently the problem is present.

[TongWu06]

Thanks for the guidance. I’m attaching the following (In Gmail):

.bash_profile
.biostar.sh
bash_startup_diagnose.txt (a consolidated report that includes my OS/Bash info, bash -n syntax checks, and the output of sourcing each file in a clean Bash session)

Notes:
My operating system is: [Windows 11 + WSL2 (Ubuntu 24.04)]

[TongWu06]

Actually, I found that my Python and doctor.py are not in the same directory

wutong@LAPTOP-TKU3BFJH ~
$ ls
bash_startup_diagnose.txt  bin  check_bash_startup.sh  edirect  micromamba
(bioinfo)
wutong@LAPTOP-TKU3BFJH ~
$ find ~ -name "doctor.py"
/home/wutong/bin/doctor.py
(bioinfo)

and then I ran doctor.py and got this result.

$ cd ~/bin
python3 doctor.py
# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa           --> ERROR
# datamash      --> ERROR
# fastqc -h     --> ERROR
# hisat2        --> ERROR
# featureCounts --> ERROR
# efetch        ... OK
# esearch       ... OK
# samtools      --> ERROR
# fastq-dump    ... OK
# bowtie2       --> ERROR
# bcftools      --> ERROR
# seqtk         --> ERROR
# seqkit        --> ERROR
# bio           --> ERROR
# fastq-dump -X 1 -Z SRR1553591 ... OK
#
# Found some problems
#
# Unable to run: bwa, datamash, fastqc -h, hisat2, featureCounts, samtools, bowtie2, bcftools, seqtk, seqkit, bio
#
# Check the Biostar Handbook for installation help.
#
(bioinfo)

[TongWu06]

I guess:Maybe the tools were installed, but that the PATH wasn’t set correctly. Even though I activated (bioinfo), the micromamba shell hook didn’t take effect in the shell, so the PATH didn’t switch to bioinfo/env/bin.
As a result, doctor.py couldn’t find them → which led to all the errors.

[TongWu06]

Actually, I have reinstalled Ubuntu multiple times, but the result is always the same. Now I’m planning to try with another computer.

[ialbert]

when you run

micromamba shell init --shell bash --root-prefix=~/.local/share/mamba

the location ~/.local/share/mamba does not exist so it cannot initialize your directory,

instead try

micromamba shell init --shell bash --root-prefix=~/micromamba/

since that is the location the handbook creates the environment in

[ialbert]

there is also a step-by-step guide that allows one to run the commands one by one to track down errors,

https://www.biostarhandbook.com/fast/setup/setup-step-by-step/

[TongWu06]

you are right, now the result is:

+ micromamba activate bioinfo
+ __mamba_wrap activate bioinfo
+ local cmd=activate
+ case "${cmd}" in
+ __mamba_xctivate activate bioinfo
+ local ask_mamba
++ PS1='\[\e]0;\w\a\]\n\[\e[32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ '
++ __mamba_exe shell activate bioinfo --shell bash
++ /home/wutong/bin/micromamba shell activate bioinfo --shell bash
+ ask_mamba='PS1='\''(bioinfo) \[\e]0;\w\a\]\n\[\e[32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ '\''
export PATH='\''/home/wutong/micromamba/envs/bioinfo/bin:/home/wutong/bin/sratoolkit.3.0.0-ubuntu64/bin:/home/wutong/bin:/home/wutong/edirect:/home/wutong/micromamba/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/mingw/bin:/mnt/c/Users/wu'\''tong/AppData/Roaming/Python/Python312/Scripts:/mnt/c/Program Files/dotnet/:/mnt/d/MATLAB/R2024b/runtime/win64:/mnt/d/MATLAB/R2024b/bin:/mnt/d/anaconda3:/mnt/d/anaconda3/Scripts:/mnt/d/anaconda3/Library/bin:/mnt/c/Program Files/PowerShell/7/:/mnt/c/Users/wt/AppData/Local/Microsoft/WindowsApps:/snap/bin'\''
export CONDA_PREFIX='\''/home/wutong/micromamba/envs/bioinfo'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''bioinfo'\''
export CONDA_PROMPT_MODIFIER='\''(bioinfo) '\''
. "/home/wutong/micromamba/envs/bioinfo/etc/conda/activate.d/libglib_activate.sh"
. "/home/wutong/micromamba/envs/bioinfo/etc/conda/activate.d/libxml2_activate.sh"
. "/home/wutong/micromamba/envs/bioinfo/etc/conda/activate.d/openjdk_activate.sh"'
+ eval 'PS1='\''(bioinfo) \[\e]0;\w\a\]\n\[\e[32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ '\''
export PATH='\''/home/wutong/micromamba/envs/bioinfo/bin:/home/wutong/bin/sratoolkit.3.0.0-ubuntu64/bin:/home/wutong/bin:/home/wutong/edirect:/home/wutong/micromamba/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/mingw/bin:/mnt/c/Users/wu'\''tong/AppData/Roaming/Python/Python312/Scripts:/mnt/c/Program Files/dotnet/:/mnt/d/MATLAB/R2024b/runtime/win64:/mnt/d/MATLAB/R2024b/bin:/mnt/d/anaconda3:/mnt/d/anaconda3/Scripts:/mnt/d/anaconda3/Library/bin:/mnt/c/Program Files/PowerShell/7/:/mnt/c/Users/wt/AppData/Local/Microsoft/WindowsApps:/snap/bin'\''
export CONDA_PREFIX='\''/home/wutong/micromamba/envs/bioinfo'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''bioinfo'\''
export CONDA_PROMPT_MODIFIER='\''(bioinfo) '\''
. "/home/wutong/micromamba/envs/bioinfo/etc/conda/activate.d/libglib_activate.sh"
. "/home/wutong/micromamba/envs/bioinfo/etc/conda/activate.d/libxml2_activate.sh"
. "/home/wutong/micromamba/envs/bioinfo/etc/conda/activate.d/openjdk_activate.sh"'
++ PS1='(bioinfo) \[\e]0;\w\a\]\n\[\e[32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ '
-bash: syntax error near unexpected token `('
+ __mamba_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ set +x
(bioinfo)

[TongWu06]

OK! I will try step-by-step install! thank u for all these day's help!