We do not have internet access on our Linux server. When executing Seeker v3.0 pipeline with Singularity, the pipeline is unable to download containers for subread, SAMtools, and STAR. This usually results in NextFlow throwing a “Join mismatch” type error. How do I solve this?
We do not have internet access on our Linux server. When executing Seeker v3.0 pipeline with Singularity, the pipeline is unable to download containers for subread, SAMtools, and STAR. This usually results in NextFlow throwing a “Join mismatch” type error. How do I solve this?
Errors Observed:
nextflow.exception.AbortOperationException: Join mismatch for the following entries…
- Follow the instructions below to solve this issue:
- Download the following file and uncompress it:
$ tar -xvf curioseeker-public-singularity-dec-2024.tar.gz
2. This file contains the containers for subread, SAMtools, and STAR. Move these containers into the .singularity cache directory (this is usually located at /home/${user_name}/.singularity/)
$ mv depot.galaxyproject.org-singularity-samtools-1.15.1–h1170115_0.img /home/user_name/.singularity/.
$ mv depot.galaxyproject.org-singularity-subread-2.0.1–hed695b0_0.img /home/user_name/.singularity/.
$ mv quay.io-biocontainers-star-2.6.1d–0.img /home/user_name/.singularity/.
3. Set the environment variable NXF_SINGULARITY_CACHEDIR equal to the full path of the .singularity directory. This is important to inform the pipeline of the location of the containers.
$ export NXF_SINGULARITY_CACHEDIR=/home/user_name/.singularity/.
4. Execute the Seeker v3.0 pipeline as normal with the profile ‘singularity’, slurm’, or ‘sge’.