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AlgoLab / galig

A graph aligner
GNU General Public License v3.0
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Docker permissions issue #11

Closed husamia closed 4 years ago

husamia commented 4 years ago

I am running into issues with group permission with docker.

docker run -v "$PWD"/input:/data algolab/asgal:v1.1.1 Starting with UID:GID 0:0 groupadd: GID '0' already exists useradd: group 'group' does not exist error: failed switching to "user:group": unable to find user user: no matching entries in passwd file

gdv commented 4 years ago

May you please include some information on your system (e.g. which operating system/distribution), and on the contents of the input dir?

husamia commented 4 years ago

May you please include some information on your system (e.g. which operating system/distribution), and on the contents of the input dir?

I am using Docker Desktop on Windows and input is the sample data

gdv commented 4 years ago

Did you also run 

wget https://github.com/AlgoLab/galig/raw/master/example/input.tar.gz
tar xfz input.tar.gz

before running asgal? The error message you got usually happens when the input directory has not been created before.

husamia commented 4 years ago

yes, I did that.

On Sun, Nov 15, 2020 at 11:53 AM Gianluca Della Vedova < notifications@github.com> wrote:

Did you also run

wget https://github.com/AlgoLab/galig/raw/master/example/input.tar.gz tar xfz input.tar.gz

before running asgal? The error message you got usually happens when the input directory has not been created before.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/AlgoLab/galig/issues/11#issuecomment-727600830, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADGRHUFPEM3X2TX6MQK3VU3SQABRVANCNFSM4TUVJEPA .

gdv commented 4 years ago

May I ask you to provide the contents (and permissions) of the current directory and of the input directory? Sorry, but I don't have a Windows machine to try to replicate your situation.

Take care

husamia commented 4 years ago

drwxrwxrwx 1 root root 4.0K Nov 25 2019 input

-rwxrwxrwx 1 root root 15K Jan 28 2018 annotation.gtf -rwxrwxrwx 1 root root 23M Jan 28 2018 genome.fa -rwxrwxrwx 1 root root 3.2M Jan 28 2018 sample_1.fa

It's not Windows problem. I am using WSL

On Mon, Nov 16, 2020 at 2:14 AM Gianluca Della Vedova < notifications@github.com> wrote:

May I ask you to provide the contents (and permissions) of the current directory and of the input directory? Sorry, but I don't have a Windows machine to try to replicate your situation.

Take care

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/AlgoLab/galig/issues/11#issuecomment-727785201, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADGRHUAPAAUUTUGWID2DO53SQDGOVANCNFSM4TUVJEPA .

gdv commented 4 years ago

Ok, then the problem is some sort of interaction with WSL. We expect that the input directory is owned by a regular user, not root. I am going to update the docker image shortly to take into account this issue. Thanks for the report.

husamia commented 4 years ago

Do you know how to pull the latest docker container with the fix?

gdv commented 4 years ago

If you delete the image with docker rmi, the next docker run should pull the updated container. You can use docker images to see the list of your images.

Take care

Gianluca Della Vedova https://gianluca.dellavedova.org On 17/11/2020 at 17:37, husamia wrote:

Do you know how to pull the latest docker container with the fix?

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husamia commented 4 years ago

When I try to delete I get an error that another container is using it but I don't have that container docker rmi d9fa1ddd9d21 Error response from daemon: conflict: unable to delete d9fa1ddd9d21 (must be forced) - image is being used by stopped container 4d03f790f96d so I force delete it and when I pull it, it seems to not pulling the latest update for some reason..

gdv commented 4 years ago

I have uploaded a new image to docker hub. May you please try docker run -v "$PWD"/input:/data algolab/asgal:v1.1.2 ?

husamia commented 4 years ago

It's working now. I can't pass arguments using interactive mode i.e. -it with docker and bash.

gdv commented 4 years ago

The docker image has not been designed for interactive use. What do you want to achieve? Maybe there is another way.

husamia commented 4 years ago

I want to do genome-wide analysis with my own data from RNA-Seq using docker container. I want to create new annotations from ensembl for GRCh38.

gdv commented 4 years ago

In this case, you should just copy your files into the input directory (or use a different directory in the -v option of docker run).

The filenames must be the same as those used in the sample dataset.

If you want to use different filenames, you need to compile asgal instead of using the docker image.

Take care.