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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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Problems with installation and usage via Docker and Singularity #397

Closed Carolinacanettieri closed 7 months ago

Carolinacanettieri commented 1 year ago

Hi Juke!

I have failed to install and use AGAT through Docker and Singularity. I have successfully installed it cloning the Git Repo and using Conda, though. I'm writing this issue to share some problems I've found while trying to use the mentioned programs, aiming to make it usefull for fixing bugs or making updates.

When I follow the recommended steps to install and run AGAT through Docker and Singularity, pulling the software image aparentely works. They return the following messages:

Docker: 1.2.0--pl5321hdfd78af_0: Pulling from biocontainers/agat 642efca944a0: Pull complete bd9ddc54bea9: Pull complete 4c206e81fe8e: Pull complete Digest: sha256:7ea8fa5a8428758cd87e3a5dcfaf277febdfcae95cd1fe473770abf8b928ec99 Status: Downloaded newer image for quay.io/biocontainers/agat:1.2.0--pl5321hdfd78af_0 quay.io/biocontainers/agat:1.2.0--pl5321hdfd78af_0

Running ---help with the suggested AGAT script using Docker also works.

Singularity: INFO: Converting OCI blobs to SIF format INFO: Starting build... Getting image source signatures Copying blob 642efca944a0 done Copying blob bd9ddc54bea9 done Copying blob 4c206e81fe8e done Copying config e45a46500f done Writing manifest to image destination Storing signatures 2023/08/31 10:52:57 info unpack layer: sha256:642efca944a099a40fb3c07af9503df633650ab4299bba89f04e2106bfe2d85e 2023/08/31 10:52:57 info unpack layer: sha256:bd9ddc54bea929a22b334e73e026d4136e5b73f5cc29942896c72e4ece69b13d 2023/08/31 10:52:57 info unpack layer: sha256:4c206e81fe8eea5a444add96a5ae6fac74590cbdbf9af53b916f50c218f20c8a INFO: Creating SIF file...

But after pulling the image, I am not able to run any AGAT script with input

Docker can't find the input and output paths and, when I add them to the options, it returns the following error: No such file or directory at /usr/local/lib/perl5/site_perl/AGAT/OmniscientO.pm line 67. It turns out that there is no /usr/local/lib/perl5/ directory.

In other hand, when running Singularity, although it indeed downloads the SIF file, the software cannot open it. It returns: FATAL: could not open image WDPATH/agat_1.2.0--pl5321hdfd78af_0: failed to retrieve path for WDPATH/agat_1.2.0--pl5321hdfd78af_0: lstat WDPATH/agat_1.2.0--pl5321hdfd78af_0: no such file or directory

I probably have some issues related to Perl in my Linux Server, but as all these programs create specific enviroments for softwares, I was not expecting to find any errors.

Juke34 commented 1 year ago

What computer do you use? What architecture ARM or X86?

Carolinacanettieri commented 1 year ago

Hi I use a Linux server x86_64

Juke34 commented 1 year ago

Ok then it is most likely a problem with your command. I will give a try to the docker image to be sure it is working properly.

Juke34 commented 9 months ago

I have not seen any problem on my side

Carolinacanettieri commented 9 months ago

Well, then it is probably some issue with my server. Thank you for your update and your dedication to improve this great tool!