diff --git a/README.md b/README.md index 4e07aa257768a76de9a5bc31e1761cc181223e24..a368a71159d3050615eb65a35949561143f5e925 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# GeVarLi: GEnome assembly, VARiant calling and LIneage assignation # +# GeVarLi: GEnome assemblyA, VARiant calling and LIneage assignation #   | Catalina (10.15.7) | Big Sure (11.6.3) | Monterey (12.6.0) | Ventura (13.3.1)/E6055C?icon=apple&label&list=|&scale=0.9>) @@ -159,7 +159,7 @@ conda update -n base -c defaults conda ### GeVarLi ### -**Clone** _to your home/_ [GeVarLi](https://forge.ird.fr/transvihmi/nfernandez/GeVarLi) GitLab IRDForge repository _(ID: 399)_ _(128Mo)_: +**Clone** _to your home/_ [GeVarLi](https://forge.ird.fr/transvihmi/nfernandez/GeVarLi) GitLab IRDForge repository _(ID: 399)_: _(128 Mo required)_ ```shell @@ -168,11 +168,17 @@ git clone --depth 1 https://forge.ird.fr/transvihmi/nfernandez/GeVarLi.git ~/GeV **Update** GeVarLi: ```shell -cd ~/GeVarLi/ && git reset --hard HEAD && git pull --verbose +cd ~/GeVarLi/ && git reset --hard HEAD && git pull --depth 1 --verbose ``` -Otherwise, you can**download** GeVarLi (no update through "git pull"): +Otherwise, you can just **download** GeVarLi (no update through "git pull"): _(75 Mo required)_ + + +<img src="./resources/visuals/download_button.png" width="400" height="100"> + +or + ```shell curl https://forge.ird.fr/transvihmi/nfernandez/GeVarLi/-/archive/main/GeVarLi-main.tar.gz -o ~/GeVarLi-main.tar.gz && \ tar -xzvf ~/GeVarLi-main.tar.gz && \ @@ -185,7 +191,7 @@ rm -f ~/GeVarLi-main.tar.gz 1. Copy your **paired-end** reads files, in **.fastq.gz** format, into: **./resources/reads/** directory _Without reads, SARS-CoV-2 from ./resources/test\_data/ directory will be used_ -2. Execute **Start_GeVarLi.sh** bash script to run GeVarLi pipeline _(according to your choice)_: +2. Execute **Start_GeVarLi.sh** bash script to run GeVarLi pipeline: - or with a **Double-click** on it _(if you make .sh files executable files with Terminal.app)_ - or with a **Right-click** > **Open with** > **Terminal.app** - or with **CLI** from a terminal: @@ -198,7 +204,7 @@ _Option-1: Edit **config.yaml** file in **./configuration/** directory_ _Option-2: Edit **fastq-screen.conf** file in **./configuration/** directory_ First run will auto-created _(only once)_: - - Workflow-Base conda environment _(with: Snakemake, Mamba, Yq, Rename and GraphViz)_ + - Workflow-Baseconda environment _(with: Snakemake, Mamba, Yq, Rename and GraphViz)_ - GeVarLi all tTools conda environments _(tools used by GeVarLi rules)_ - Indexes for BWA and BOWTIE2 aligners _(for each fasta genomes in resources/ directory)_ @@ -285,9 +291,9 @@ _Some [temp] tagged files are removed by default, to save disk usage_  ├── âš™ï¸ config.log  ├── 📠settings.log  ├── 🜠gevarli-base_v.{VERSION}.yaml -  ├── 🜠gevarli-tools_v.{VERSION}.yaml + ├── 📂 conda_env/ +  │ └── 📄 {TOOLS}_v.{version}.yaml ├── 📂 files-summaries -  │ └── 📄 {PIPELINE}_files-summary.txt  ├── 📂 graphs/  │ ├── 📈 {PIPELINE}_dag.{PNG/PDF}  │ ├── 📈 {PIPELINE}_filegraph.{PNG/PDF} @@ -565,8 +571,7 @@ _F1000Research (2021)_ **Documentation**: [https://snakemake.readthedocs.io/en/stable/index.html](https://snakemake.readthedocs.io/en/stable/index.html) **Anaconda Software Distribution** -Team -_Computer software (2016)_ +_Team-Computer software (2016)_ **DOI**: []() **Publication**: [https://www.anaconda.com](https://www.anaconda.com) **Source code**: [https://github.com/snakemake/snakemake](https://github.com/snakemake/snakemake) (conda) diff --git a/resources/visuals/download_button.png b/resources/visuals/download_button.png new file mode 100644 index 0000000000000000000000000000000000000000..959269cf83f3787f29c8679686e0aab67576b509 Binary files /dev/null and b/resources/visuals/download_button.png differ