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posts/IMAM-02-preparation.qmd

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This workflow is distributed as a self-contained Singularity container image, which includes all necessary software dependencies and helper scripts. This simplifies setup considerably. It is required that [Singularity](https://docs.sylabs.io/guides/3.5/user-guide/introduction.html){target="_blank"} version 3.x or later is available on your system. If you are working with a high performance computing (HPC) system, then this will likely already be installed and available for use. Try writing `singularity --help` in your terminal (that's connected to the HPC system) and see if the command is recognized.
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### 1.1.1 Download pre-built image {.unnumbered}
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## 1.2 Download pre-built image {.unnumbered}
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The singularity container needs an image file to activate the precompiled work environment. You can download the required workflow image file (imam_workflow.sif) directly through the terminal via:
2020

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Or go to the [github page](https://github.com/LucvZon/illumina-metagenomic-analysis-manual/releases/tag/v1.0.1){target="_blank"} and manually download it there, then transfer it to your HPC system.
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### 1.1.2 Verify container {.unnumbered}
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## 1.3 Verify container {.unnumbered}
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You can test basic execution:
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posts/NAAM-02-preparation.qmd

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Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ Notice the small *"Copy to Clipboard"* button on the right hand side of each cod
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This workflow is distributed as a self-contained Singularity container image, which includes all necessary software dependencies and helper scripts. This simplifies setup considerably. It is required that [Singularity](https://docs.sylabs.io/guides/3.5/user-guide/introduction.html){target="_blank"} version 3.x or later is available on your system. If you are working with a high performance computing (HPC) system, then this will likely already be installed and available for use. Try writing `singularity --help` in your terminal (that's connected to the HPC system) and see if the command is recognized.
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### Download pre-built image
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## 1.2 Download pre-built image
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The singularity container needs an image file to activate the precompiled work environment. You can download the required workflow image file (naam_workflow.sif) directly through the terminal via:
2020

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Or go to the [github page](https://github.com/LucvZon/nanopore-amplicon-analysis-manual/releases/tag/v1.0.0){target="_blank"} and manually download it there, then transfer it to your HPC system.
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### 1.2 Verify container {.unnumbered}
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## 1.3 Verify container {.unnumbered}
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You can test basic execution:
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