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jfy133 merged 1 commit into from
Sep 19, 2025
Merged

Update all chapter dataset links to new Zenodo uploads for 2025 updated datasets #131

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2 changes: 1 addition & 1 deletion accessing-ancient-metagenomic-data.qmd
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Expand Up @@ -10,7 +10,7 @@ bibliography: assets/references/accessing-ancient-metagenomic-data.bib
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759163](https://doi.org/10.5281/zenodo.13759163), and unpack
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155430](https://doi.org/10.5281/zenodo.17155430), and unpack

```bash
tar xvf accessing-ancient-metagenomic-data.tar.gz
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2 changes: 1 addition & 1 deletion ancient-metagenomic-pipelines.qmd
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Expand Up @@ -8,7 +8,7 @@ bibliography: assets/references/ancient-metagenomic-pipelines.bib
For this chapter's exercises, if not already performed, we will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive:
[10.5281/zenodo.13759201](https://doi.org/10.5281/zenodo.13759201), and unpack.
[10.5281/zenodo.17155341](https://doi.org/10.5281/zenodo.17155341), and unpack.

```bash
tar xvf ancient-metagenomic-pipelines.tar.gz
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2 changes: 1 addition & 1 deletion authentication.qmd
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Expand Up @@ -7,7 +7,7 @@ bibliography: assets/references/authentication.bib
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759228](https://doi.org/10.5281/zenodo.13759228), and unpack
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17152964](https://doi.org/10.5281/zenodo.17152964), and unpack

```bash
tar xvf authentication.tar.gz
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2 changes: 1 addition & 1 deletion bare-bones-bash.qmd
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Expand Up @@ -6,7 +6,7 @@ author: Thiseas C. Lamnidis, Aida Andrades Valtueña
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759270](https://doi.org/10.5281/zenodo.13759270), and unpack.
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155440](https://doi.org/10.5281/zenodo.17155440), and unpack.

```bash
tar xvf bare-bones-bash.tar.gz
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2 changes: 1 addition & 1 deletion contamination.qmd
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Expand Up @@ -7,7 +7,7 @@ bibliography: assets/references/contamination.bib
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759285](https://doi.org/10.5281/zenodo.13759285), and unpack
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155413](https://doi.org/10.5281/zenodo.17155413), and unpack

```bash
tar xvf contamination.tar.gz
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2 changes: 1 addition & 1 deletion denovo-assembly.qmd
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Expand Up @@ -13,7 +13,7 @@ library(pander)
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759302](https://doi.org/10.5281/zenodo.13759302), and unpack
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17142958](https://doi.org/10.5281/zenodo.17142958), and unpack

```bash
tar xvf denovo-assembly.tar.gz
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2 changes: 1 addition & 1 deletion genome-mapping.qmd
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Expand Up @@ -7,7 +7,7 @@ bibliography: assets/references/genome-mapping.bib
:::{.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759321](https://doi.org/10.5281/zenodo.13759321), and unpack.
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17154630](https://doi.org/10.5281/zenodo.17154630), and unpack.

```bash
tar xvf genome-mapping.tar.gz
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2 changes: 1 addition & 1 deletion git-github.qmd
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Expand Up @@ -7,7 +7,7 @@ bibliography: assets/references/git-github.bib
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759333](https://doi.org/10.5281/zenodo.13759333), and unpack.
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155418](https://doi.org/10.5281/zenodo.17155418), and unpack.

```bash
tar xvf git-github.tar.gz
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2 changes: 1 addition & 1 deletion phylogenomics.qmd
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Expand Up @@ -7,7 +7,7 @@ bibliography: assets/references/phylogenomics.bib
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759782](https://doi.org/10.5281/zenodo.13759782), and unpack.
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155402](https://doi.org/10.5281/zenodo.17155402), and unpack.

```bash
tar xvf phylogenomics.tar.gz
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2 changes: 1 addition & 1 deletion python-pandas.qmd
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Expand Up @@ -10,7 +10,7 @@ This session is typically ran held in parallel to the Introduction to R and Tidy
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.11394586](https://doi.org/10.5281/zenodo.11394586), and unpack
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155406](https://doi.org/10.5281/zenodo.17155406), and unpack

```bash
tar xvf python-pandas.tar.gz
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2 changes: 1 addition & 1 deletion r-tidyverse.qmd
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Expand Up @@ -19,7 +19,7 @@ We recommend this session if you have no experience with neither R nor Python.
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

To do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13758879](https://doi.org/10.5281/zenodo.13758879), and unpack
To do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155415](https://doi.org/10.5281/zenodo.17155415), and unpack

```bash
tar xvf r-tidyverse.tar.gz
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2 changes: 1 addition & 1 deletion taxonomic-profiling.qmd
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Expand Up @@ -7,7 +7,7 @@ bibliography: assets/references/taxonomic-profiling.bib
::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.

Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13760277](https://doi.org/10.5281/zenodo.13760277), and unpack
Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155271](https://doi.org/10.5281/zenodo.17155271), and unpack

```bash
tar xvf taxonomic-profiling.tar.gz
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