From 6af33eae52eb16b1f1d62c00f154716fac452ee8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 16 Sep 2024 12:48:56 +0200 Subject: [PATCH] Update all DOIs to point to this years data --- accessing-ancient-metagenomic-data.qmd | 2 +- ancient-metagenomic-pipelines.qmd | 3 ++- authentication.qmd | 2 +- bare-bones-bash.qmd | 2 +- contamination.qmd | 2 +- denovo-assembly.qmd | 2 +- genome-mapping.qmd | 2 +- git-github.qmd | 2 +- phylogenomics.qmd | 2 +- python-pandas.qmd | 2 +- r-tidyverse.qmd | 2 +- taxonomic-profiling.qmd | 2 +- 12 files changed, 13 insertions(+), 12 deletions(-) diff --git a/accessing-ancient-metagenomic-data.qmd b/accessing-ancient-metagenomic-data.qmd index a5297ae2..da466b4e 100644 --- a/accessing-ancient-metagenomic-data.qmd +++ b/accessing-ancient-metagenomic-data.qmd @@ -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.8413229](https://doi.org/10.5281/zenodo.8413229), and unpack +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 ```bash tar xvf accessing-ancient-metagenomic-data.tar.gz diff --git a/ancient-metagenomic-pipelines.qmd b/ancient-metagenomic-pipelines.qmd index 97ba56e3..100ea8d9 100644 --- a/ancient-metagenomic-pipelines.qmd +++ b/ancient-metagenomic-pipelines.qmd @@ -7,7 +7,8 @@ bibliography: assets/references/ancient-metagenomic-pipelines.bib ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"} 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.8413239](https://doi.org/10.5281/zenodo.8413239), and unpack. +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. ```bash tar xvf ancient-metagenomic-pipelines.tar.gz diff --git a/authentication.qmd b/authentication.qmd index bb6fe2c1..b1f00226 100644 --- a/authentication.qmd +++ b/authentication.qmd @@ -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.8413184](https://doi.org/10.5281/zenodo.8413184), and unpack +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 ```bash tar xvf authentication.tar.gz diff --git a/bare-bones-bash.qmd b/bare-bones-bash.qmd index efbaf944..79e414e2 100644 --- a/bare-bones-bash.qmd +++ b/bare-bones-bash.qmd @@ -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.8412661](https://doi.org/10.5281/zenodo.8412661), and unpack. +Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759270](10.5281/zenodo.13759270), and unpack. ```bash tar xvf bare-bones-bash.tar.gz diff --git a/contamination.qmd b/contamination.qmd index 0c050f12..5800b561 100644 --- a/contamination.qmd +++ b/contamination.qmd @@ -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.8413184](https://doi.org/10.5281/zenodo.8413184), and unpack +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 ```bash tar xvf contamination.tar.gz diff --git a/denovo-assembly.qmd b/denovo-assembly.qmd index 8b049a82..c7f5afcd 100644 --- a/denovo-assembly.qmd +++ b/denovo-assembly.qmd @@ -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.8413147](https://doi.org/10.5281/zenodo.8413147), and unpack +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 ```bash tar xvf denovo-assembly.tar.gz diff --git a/genome-mapping.qmd b/genome-mapping.qmd index 3c16f3e3..b1891071 100644 --- a/genome-mapping.qmd +++ b/genome-mapping.qmd @@ -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.8413204](https://doi.org/10.5281/zenodo.8413204), and unpack. +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. ```bash tar xvf genome-mapping.tar.gz diff --git a/git-github.qmd b/git-github.qmd index 6322f6dd..cc7d55ca 100644 --- a/git-github.qmd +++ b/git-github.qmd @@ -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.8413100](https://doi.org/10.5281/zenodo.8413100), and unpack. +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. ```bash tar xvf git-github.tar.gz diff --git a/phylogenomics.qmd b/phylogenomics.qmd index 17fed2cf..57d1f658 100644 --- a/phylogenomics.qmd +++ b/phylogenomics.qmd @@ -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.8413215](https://doi.org/10.5281/zenodo.8413215), and unpack. +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. ```bash tar xvf phylogenomics.tar.gz diff --git a/python-pandas.qmd b/python-pandas.qmd index 4503d417..bd29016b 100644 --- a/python-pandas.qmd +++ b/python-pandas.qmd @@ -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.8413046](https://doi.org/10.5281/zenodo.8413046), and unpack +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 ```bash tar xvf python-pandas.tar.gz diff --git a/r-tidyverse.qmd b/r-tidyverse.qmd index af96fdc5..a4a1f6ea 100644 --- a/r-tidyverse.qmd +++ b/r-tidyverse.qmd @@ -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.8413026](https://doi.org/10.5281/zenodo.8413026), and unpack +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 ```bash tar xvf r-tidyverse.tar.gz diff --git a/taxonomic-profiling.qmd b/taxonomic-profiling.qmd index db98f495..36414181 100644 --- a/taxonomic-profiling.qmd +++ b/taxonomic-profiling.qmd @@ -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.8413138](https://doi.org/10.5281/zenodo.8413138), and unpack +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 ```bash tar xvf taxonomic-profiling.tar.gz