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Can't use metaWRAP after installation #587

@ShevchenkoAlla

Description

@ShevchenkoAlla

Hi!
I think I have installed the metawrap,
Using this way -

Download or clone this ripository: git clone https://github.com/bxlab/metaWRAP.git
Carefully configure the yourpath/metaWRAP/bin/config-metawrap file to it points to your desired database locations (you can modify this later). Follow the database configuration guide for details.
Make metaWRAP executable by adding yourpath/metaWRAP/bin/ directory to to your $PATH. Either add the line PATH=yourpath/metaWRAP/bin/:$PATH to your ~/.bash_profile script, or copy over the contents of yourpath/metaWRAP/bin/ into a location already in your $PATH (such as /usr/bin/ or /miniconda2/bin/).

Now I have a folder, and some db...

metawrap -h

MetaWRAP v=1.3.2

I don't have metawrap-env, just the folder

When I try to run read_qc, I got error-

/usr/bin/env: 'python2.7': No such file or directory

real 0m0.035s
user 0m0.010s
sys 0m0.009s
/usr/bin/env: 'python2.7': No such file or directory
/usr/bin/env: 'python2.7': No such file or directory
real 0m0.038s
user 0m0.007s
sys 0m0.012s

real 0m0.037s
user 0m0.005s
sys 0m0.012s

I can't understand why it keep looking for the python in env folder

I have tried a few things but it didn't worked,
like - find . -name "*.py" -type f -exec sed -i '1s|#!/usr/bin/env python2.7|#!/usr/bin/python2|' {} +

and put the next in the script, we have a slurm system
mkdir -p /tmp/python_fix_${SLURM_JOB_ID}
ln -sf /usr/bin/python2.7 /tmp/python_fix_${SLURM_JOB_ID}/python2.7
export PATH="/tmp/python_fix_${SLURM_JOB_ID}:$PATH"

echo "=== Python check ==="
/usr/bin/env python2.7 --version

export PATH="/home/shevch_alla/beegfs/shevch_alla/metaWRAP/bin:$PATH"

But I do have python,

/usr/bin/env python2.7 --version
Python 2.7.18

ls -la /usr/bin/python*
lrwxrwxrwx. 1 root root 9 окт 15 2024 /usr/bin/python2 -> python2.7
-rwxr-xr-x. 1 root root 8160 апр 21 2022 /usr/bin/python2.7
lrwxrwxrwx. 1 root root 25 окт 15 2024 /usr/bin/python3 -> /etc/alternatives/python3
lrwxrwxrwx. 1 root root 31 окт 15 2024 /usr/bin/python3.6 -> /usr/libexec/platform-python3.6
lrwxrwxrwx. 1 root root 32 окт 15 2024 /usr/bin/python3.6m -> /usr/libexec/platform-python3.6m
-rwxr-xr-x. 1 root root 2570 ноя 13 2019 /usr/bin/python-argcomplete-check-easy-install-script
-rwxr-xr-x. 1 root root 314 ноя 16 2017 /usr/bin/python-argcomplete-tcsh

None of it worked

Do anyone have any suggestions how to fix this?

Thanks,
Alla

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