From 1fbc9d8c72713e4d33084e96058ad2e04f05955a Mon Sep 17 00:00:00 2001 From: Roy Francis Date: Mon, 6 Jan 2025 20:21:56 +0100 Subject: [PATCH] Renamed reseq to vc, removed old dockerfile --- README.md | 4 +-- Dockerfile => dockerfile | 0 scripts/Dockerfile | 34 ------------------- scripts/{reseq => vc}/best_practise.sbatch | 0 scripts/{reseq => vc}/joint_genotyping.sbatch | 0 .../{reseq => vc}/vc_basic_pipeline.sbatch | 0 scripts/{reseq => vc}/vc_bp_pipeline.sbatch | 0 scripts/{reseq => vc}/vc_pipeline.sbatch | 0 8 files changed, 2 insertions(+), 36 deletions(-) rename Dockerfile => dockerfile (100%) delete mode 100644 scripts/Dockerfile rename scripts/{reseq => vc}/best_practise.sbatch (100%) rename scripts/{reseq => vc}/joint_genotyping.sbatch (100%) rename scripts/{reseq => vc}/vc_basic_pipeline.sbatch (100%) rename scripts/{reseq => vc}/vc_bp_pipeline.sbatch (100%) rename scripts/{reseq => vc}/vc_pipeline.sbatch (100%) diff --git a/README.md b/README.md index f4221b84f..c17f1360b 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,7 @@ as the first thing, so that old rendered files are not overwritten. You can preview changes and build the whole website locally without a local installation of R or dependency packages by using the pre-built Docker image. -:exclamation: **Note:** Large image size: 4.68GB. +:exclamation: **Note:** Image size: 4.86GB. Clone the repo if not already done. Make sure you are standing in the repo directory. @@ -91,7 +91,7 @@ This repo is loosely based on the quarto template [specky](https://github.com/ro ## Test scripts -This is regarding the directory **scripts**. This directory contains shell scripts for reseq (variant-calling) and rnaseq parts of the workshop. These are intended to be run on UPPMAX. Further instructions on using them are available within the scripts. +This is regarding the directory **scripts**. This directory contains shell scripts for vc (variant-calling) and rnaseq parts of the workshop. These are intended to be run on UPPMAX. Further instructions on using them are available within the scripts. The contents of these scripts should use identical steps and tools as the student would use in the lab. The aim of these scripts is to execute them on UPPMAX before the course. This should provide insight into broken links, broken tools, tool incompatibilities, core usage, ram usage and total space used. diff --git a/Dockerfile b/dockerfile similarity index 100% rename from Dockerfile rename to dockerfile diff --git a/scripts/Dockerfile b/scripts/Dockerfile deleted file mode 100644 index 052f8963c..000000000 --- a/scripts/Dockerfile +++ /dev/null @@ -1,34 +0,0 @@ -# DOCKER FILE FOR WORKSHOP-NGSINTRO -# 2023 Roy Francis - -FROM rocker/verse:4.2.3 -LABEL Description="Docker image for NBIS workshop" -LABEL Maintainer="roy.francis@nbis.se" -LABEL org.opencontainers.image.source="https://github.com/NBISweden/workshop-ngsintro" -ARG QUARTO_VERSION="1.3.433" - -RUN apt-get update -y \ - && apt-get install --no-install-recommends -y \ - libxml2-dev \ - libssl-dev \ - libcurl4-openssl-dev \ - libudunits2-dev \ - libopenblas-base \ - libgdal-dev \ - && wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb \ - && apt-get install -y ./google-chrome-stable_current_amd64.deb \ - && rm -rf ./google-chrome-stable_current_amd64.deb \ - && curl -o quarto-linux-amd64.deb -L https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb \ - && apt-get install -y ./quarto-linux-amd64.deb \ - && rm -rf ./quarto-linux-amd64.deb \ - && Rscript -e 'install.packages(c("remotes","here","htmlTable","leaflet"),repos = "http://cran.us.r-project.org");' \ - && rm -rf /var/lib/apt/lists/* \ - && mkdir /qmd - -RUN Rscript -e 'BiocManager::install(c("DESeq2","edgeR","goseq","GO.db","org.Mm.eg.db","reactome.db"));' -WORKDIR /qmd -ENV XDG_CACHE_HOME=/tmp/quarto_cache_home -ENV XDG_DATA_HOME=/tmp/quarto_data_home -CMD quarto render - - diff --git a/scripts/reseq/best_practise.sbatch b/scripts/vc/best_practise.sbatch similarity index 100% rename from scripts/reseq/best_practise.sbatch rename to scripts/vc/best_practise.sbatch diff --git a/scripts/reseq/joint_genotyping.sbatch b/scripts/vc/joint_genotyping.sbatch similarity index 100% rename from scripts/reseq/joint_genotyping.sbatch rename to scripts/vc/joint_genotyping.sbatch diff --git a/scripts/reseq/vc_basic_pipeline.sbatch b/scripts/vc/vc_basic_pipeline.sbatch similarity index 100% rename from scripts/reseq/vc_basic_pipeline.sbatch rename to scripts/vc/vc_basic_pipeline.sbatch diff --git a/scripts/reseq/vc_bp_pipeline.sbatch b/scripts/vc/vc_bp_pipeline.sbatch similarity index 100% rename from scripts/reseq/vc_bp_pipeline.sbatch rename to scripts/vc/vc_bp_pipeline.sbatch diff --git a/scripts/reseq/vc_pipeline.sbatch b/scripts/vc/vc_pipeline.sbatch similarity index 100% rename from scripts/reseq/vc_pipeline.sbatch rename to scripts/vc/vc_pipeline.sbatch