How to run in singularity?

[zckoo007]

Hi

I run on the server，but I don't have root

singularity pull docker://brinkmanlab/islandpath:latest

[ckzhu@vm-login02 islandpath]$ /public/software/apps/singularity/3.5.2/bin/singularity exec islandpath_latest.sif /apps/islandpath/Dimob.pl /apps/islandpath/example/NC_003210.gbk NC_GIs.txt
/apps/islandpath/logger.conf2021/06/10 10:45:04 [main] Logging initialized
2021/06/10 10:45:04 [main] Creating temp directory with needed files
Error creating temp directory from template /apps/islandpath/example/dimob_tmpXXXXXXXXXX: Could not create directory /apps/islandpath/example/dimob_tmpaDGWl2jKtv: Read-only file system at /apps/islandpath/Dimob.pl line 104.

singularity contain is not writble, how to wirte log and tmp files out?

[innovate-invent]

Hello, and thanks for your interest in islandpath.

When running a container, you need to bind paths from the host system into the container to write to. See https://sylabs.io/guides/3.0/user-guide/bind_paths_and_mounts.html#user-defined-bind-paths

Please let me know if this resolves your issue.

[mmfacun]

Hello.

I tried pulling both available docker images:

I tried to run a container, but the containers i run immediately exits on their own..

It's no use if i manually start the container again.. they just exit immediately.

I'm doing a bit of trial and error here..

I use docker within conda.. And i always do this with all of my analyses, but this is the first time this happened. I'm new to coding, so please help.

Thank you,

[innovate-invent]

Hi @mmfacun, and thank you for your interest in islandpath.

Please use quay.io/biocontainers/islandpath:1.0.6--hdfd78af_0 as the source of the image.

Also, execute it as docker run --rm -v"$(pwd):$(pwd)" quay.io/biocontainers/islandpath:1.0.6--hdfd78af_0 islandpath <input> <output>

[mmfacun]

Thank you. I got it working