Questions tagged [singularity]

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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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1 answer
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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 ...
Indira's user avatar
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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 ...
Indira's user avatar
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1 vote
1 answer
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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 ...
Indira's user avatar
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2 answers
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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: ...
Indira's user avatar
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1 vote
1 answer
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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 ...
Indira's user avatar
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3 votes
1 answer
247 views

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: ...
Indira's user avatar
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2 votes
1 answer
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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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