singularity about ksrates HOT 5 CLOSED

Thank you so much for answering my stupid question, I'm going to try to download Docker and run it again.

Because it prompted me that the singularity command was not found, I saw a Singularity under your directory, I foolishly thought that this 'S' ingularity could be used after changing it to 's' ingularity, and then a series of errors appeared.

from ksrates.

Is the singularity provided by your project available? Do I need to download it myself？but I don't have administrator rights

from ksrates.

singularity pull --name vibpsb-ksrates-latest.img docker://vibpsb/ksrates:latest after running.
like this
/share/home/stu_wangtianyou/soft/ksrates/singularity: line 1: Bootstrap:: command not found /share/home/stu_wangtianyou/soft/ksrates/singularity: line 2: From:: command not found /share/home/stu_wangtianyou/soft/ksrates/singularity: line 4: fg: no job control /share/home/stu_wangtianyou/soft/ksrates/singularity: line 5: AUTHOR: command not found /share/home/stu_wangtianyou/soft/ksrates/singularity: line 7: fg: no job control /share/home/stu_wangtianyou/soft/ksrates/singularity: line 8: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8): No such file or directory /share/home/stu_wangtianyou/soft/ksrates/singularity: line 8: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) /share/home/stu_wangtianyou/soft/ksrates/singularity: line 12: fg: no job control bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) /share/home/stu_wangtianyou/soft/ksrates/requirements.txt: line 9: scikit-learn==0.24.2: command not found bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) /share/home/stu_wangtianyou/soft/ksrates/setup.py: line 1: from: command not found /share/home/stu_wangtianyou/soft/ksrates/setup.py: line 2: from: command not found /share/home/stu_wangtianyou/soft/ksrates/setup.py: line 4: syntax error near unexpected token ('
/share/home/stu_wangtianyou/soft/ksrates/setup.py: line 4: with open("README.md", 'r') as f:' /share/home/stu_wangtianyou/soft/ksrates/singularity: line 15: ksrates: command not found /share/home/stu_wangtianyou/soft/ksrates/singularity: line 16: wgd_ksrates: command not found bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) /share/home/stu_wangtianyou/soft/ksrates/README.md: line 1: syntax error near unexpected token ('
/share/home/stu_wangtianyou/soft/ksrates/README.md: line 1: [![Test pipeline CI](https://github.com/VIB-PSB/ksrates/actions/workflows/test_pipeline.yml/badge.svg)](https://github.com/VIB-PSB/ksrates/actions/workflows/test_pipeline.yml)' bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) /share/home/stu_wangtianyou/soft/ksrates/ksrates_cli.py: line 1: import: command not found /share/home/stu_wangtianyou/soft/ksrates/ksrates_cli.py: line 2: import: command not found /share/home/stu_wangtianyou/soft/ksrates/ksrates_cli.py: line 3: from: command not found /share/home/stu_wangtianyou/soft/ksrates/ksrates_cli.py: line 4: from: command not found /share/home/stu_wangtianyou/soft/ksrates/ksrates_cli.py: line 6: syntax error near unexpected token context_settings={'help_option_names':'
/share/home/stu_wangtianyou/soft/ksrates/ksrates_cli.py: line 6: @click.group(context_settings={'help_option_names': ['-h', '--help']})' /share/home/stu_wangtianyou/soft/ksrates/singularity: line 20: fg: no job control /share/home/stu_wangtianyou/soft/ksrates/singularity: line 24: apt-get: command not found /share/home/stu_wangtianyou/soft/ksrates/singularity: line 29: apt-get: command not found ERROR: Directory '/install' is not installable. Neither 'setup.py' nor 'pyproject.toml' found.
I think I should have submitted a stupid question, sorry.
I changed your Singularity to singularity, I thought it was usable.

from ksrates.

The Singularity image is available on Docker Hub, and you don't need administration rights to download and use it. Normally the Nextflow pipeline downloads it while running ksrates the first time; you can else download (pull) the image yourself in advance and tell Nextflow to use it from the Nextflow configuration file (see docs).

Many of those error lines above seem to involve the singularity file in the ksrates directory, which is just a file to make the image (for which you do need sudo rights). You can ignore that file and use the image on Docker Hub.

I'm sorry I don't understand your last comment: "I changed your Singularity to singularity, I thought it was usable." Could you rephrase it?

from ksrates.

Hi, I will now close this issue. Feel free to post another one if something else comes up!

from ksrates.