Question about using Conda (and singularity) in SGE cluster #5292
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tanyasarkjain
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Hi all,
I'm trying to use some Conda packages in my nextflow pipeline, and I'm having trouble getting Conda to work. Apologies if this question has been answered already - I looked at some passed issues on Git, and couldn't find someone with the same problem as me - I am new to using Conda with nextflow.
I have tried a few different things.For one, in my nextflow.config file, under my processes section, I tried enabling Conda, via Conda.enabled = true, and then in my nextflow script, in the specific task that I wanted to use a Conda package, I put conda "bwa samtools hiphase" to specify a Conda environment with those packages, be created. I also tried, creating a Conda profile in my nextflow.config file, where I enabled Conda, and specified which packages to use.
Would appreciate any insight for how to correctly go about this - Conda also works locally on the development node I am using.
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