Questions tagged [singularity]
The singularity tag has no usage guidance.
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Error in snakemake when running conda envs in container
I am facing an issue when running snakemake with a container and conda.
Let me explain better.
I am developing a workflow (locally) in snakemake, where some rules use a conda env (defined in /envs/env....
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87
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Singularity, AnnotSV and HPO
I am trying to use AnnotSV to annotate some Manta outputs in the following code with the HPO term changed:
Where:
input_dir is the input directory
singularity_container is the path to the AnnotSV ...
- 380
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189
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Singularity And MacOS
I am trying to install Singularity on my MacOS but it doesn't seem to pick up which singularity or singularity --version:
Main ...
- 380
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Singularity and Illumina's Nirvana
I am trying to using Illumina's Nirvana however I can't seem to get it to work despite having the right Singularity path.
I pulled Nirvana down using
...
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2
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Singularity And CNV Kit
I would like to try an use Singularity with CNV kit as the HPC I use seems to work better with Singularity:
Initial Attempt:
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GATK SplitIntervals: A USER ERROR has occurred: but no positional argument is defined for this tool
I am trying to create a GATK g CNV pipeline and I need to make shards before running the GermlineCNVCaller therefore, I believe I need to use ...
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1
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Singularity & Picard
I am trying to run Picard in Singularity and try as I might I cannot seem to find the path to use. For example with GATK 4.4.0.0 I use the following path:
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Singularity & GATK 4.4.0.0. CreateSequenceDictionary
I ran the following code in bash (I added print statements for ease):
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