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Hi,
I installed genome-seek through conda:
mamba create -c conda-forge -c bioconda -p /mycondaEnv/snakemake_singularity snakemake singularity
git clone https://github.com/OpenOmics/genome-seek.git
cd genome-seek
mamba activate /mycondaEnv/snakemake_singularity
./genome-seek --version
genome-seek 0.3.3-alpha
snakemake --version
7.25.0
singularity --version
singularity version 3.8.6
But when I tried to run: /genome-seek/genome-seek cache --sif-cache /sif-cache, I got the following error:
genome-seek (0.3.3-alpha)
Image will be pulled from "/data/OpenOmics/SIFs/ccbr_wes_base_v0.1.0.sif".
Image will be pulled from "/data/OpenOmics/SIFs/deepvariant_1.3.0-gpu.sif".
Image will be pulled from "/data/OpenOmics/SIFs/glnexus_v1.4.1.sif".
Image will be pulled from "/data/OpenOmics/SIFs/ncbr_opencravat_latest.sif".
Image will be pulled from "/data/OpenOmics/SIFs/ncbr_octopus_v0.1.0.sif".
Image will be pulled from "/data/OpenOmics/SIFs/ncbr_sigprofiler_v0.1.0.sif".
Image will be pulled from "/data/OpenOmics/SIFs/ncbr_vcf2maf_v0.1.0.sif".
/projectsp/foran/yc790/apps/genome-seek/src/cache.sh: line 210: SLURM_JOB_ID: unbound variable
/projectsp/foran/yc790/apps/genome-seek/src/cache.sh: line 210: SLURM_JOB_ID: unbound variable
WARNING: Failed to run 'set -euo pipefail; /genome-seek/src/cache.sh local -s '/sif-cache' -i '/data/OpenOmics/SIFs/ccbr_wes_base_v0.1.0.sif,/data/OpenOmics/SIFs/deepvariant_1.3.0-gpu.sif,/data/OpenOmics/SIFs/glnexus_v1.4.1.sif,/data/OpenOmics/SIFs/ncbr_opencravat_latest.sif,/data/OpenOmics/SIFs/ncbr_octopus_v0.1.0.sif,/data/OpenOmics/SIFs/ncbr_sigprofiler_v0.1.0.sif,/data/OpenOmics/SIFs/ncbr_vcf2maf_v0.1.0.sif' -t '/sif-cache/yc790/.singularity/' ' command!
└── Command returned a non-zero exitcode of '1'.
Fatal: Failed to pull all containers. Please try again!
It seems that the image sif files are missing and the SLURM_JOB_ID in cache.sh is not defined. Is there a way to get around?
Thanks a lot!
Ying
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