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ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline
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installation of some or all of components failed. #220

Closed Ahmer1122 closed 1 year ago

Ahmer1122 commented 1 year ago

Hello I am trying to install PGAP however i am getting this issue.

The latest version of PGAP is 2022-08-11.build6275, you have nothing installed locally. installation directory: /home/szweda/.pgap Filesystem 1K-blocks Used Available Use% Mounted on /dev/nvme0n1p5 452444768 78240396 351147988 19% / Skipping already installed tarball: https://s3.amazonaws.com/pgap/input-2022-08-11.build6275.tgz Downloading (as needed) Docker image ncbi/pgap:2022-08-11.build6275 Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/images/create?fromImage=ncbi%2Fpgap&tag=2022-08-11.build6275": dial unix /var/run/docker.sock: connect: permission denied None installation of some or all of components failed. Please remove /home/szweda/.pgap/input-2022-08-11.build6275, /home/szweda/.pgap/test_genomes, /home/szweda/.pgap/test_genomes-2022-08-11.build6275 directories and try again.

Using ./pgap.py -h command is working but have no other directories like input and test data.

azat-badretdin commented 1 year ago

Thank you, Ahmer, for your report!

It looks like you tried this over existing installation. Have you tried to clean the disk space occupied by the previous attempt to install 2022-08-11 release and install it again?

Actually, I see that you created an issue #221 which implies that you successfully installed PGAPx. Please let me know if that is true, so I resolve this.

Ahmer1122 commented 1 year ago

Dear Azat, thank you for your response.

Yes, I managed to solve the issue.

Thanks :)

azat-badretdin commented 1 year ago

You are welcome! :-)