NCBI PGAP yami file

Question

[Pegasus]

Hi all,

in the NCBI PGAP using-guide, they mentioned that using this pipeline requires three files;

A fasta file. A YAML file containing metadata (usually called submol.yaml). A YAML file that describes the pipeline inputs, including the above two files.

However, I have only the fasta file generated after removing the scaffolds <200 bp.

So where can I find these yaml files !!

Also, after installation on Linux, I tried to run the tool ./pgap.py or pgap.py, but I got this error :

pgap.py: command not found

Any hint !!!

[ahmedbanhawy]

Hello, I got the same errors when installing the Linux on my virtual machine you should follow the following steps in the following link

https://docs.docker.com/engine/install/ubuntu/ when you arrive to the SET UP THE REPOSITORY be careful at step no. (3) please note that the command is incorrectly line-wrapped which introduces line breaks and backslash characters where there should be none. The correct command would be:

sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"

then follow the previous link normally.

I still need to know how I could get the YAML files for gene annotation, please let me know if you get an answer

best regards

[ahmer]

Hi Ahmed, can you please rewrite the command again? i could not get it where it is incorrect.

echo \ "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \ $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

[Optimist]

I have a similar query.

I want to generate submol.yaml file for my NCBI-PGAP annotated genomes.

How to generate these yaml files.

Thank You

Answer 1

[gmreed]

Hi,

I think you want the submol.yaml file. It gives NCBI author and genome metadata. The link to the file you'll recreate is https://github.com/ncbi/pgap/blob/master/user_genome/submol.yaml

Maybe the strain and taxon are from the closest relative.

[Pegasus]

Thank you @gmreed