From 814c4f82c40a2ba49f31a18e0359cff1f4f397f0 Mon Sep 17 00:00:00 2001 From: bioaddict Date: Tue, 14 Nov 2023 10:29:02 +0100 Subject: [PATCH] Improve the README.md --- .gitignore | 9 +++++++-- README.md | 12 ++++++------ 2 files changed, 13 insertions(+), 8 deletions(-) diff --git a/.gitignore b/.gitignore index 5d947ca..6c695b3 100644 --- a/.gitignore +++ b/.gitignore @@ -6,13 +6,18 @@ bin-release/ # Other files and folders .settings/ +./data/OUT_DIR/* -# Executables +# files with extension *.swf *.air *.ipa *.apk - +*.log +*.fast5 +*.fastq +*.fastq.gz +*.fasta # Project files, i.e. `.project`, `.actionScriptProperties` and `.flexProperties` # should NOT be excluded as they contain compiler settings and other important # information for Eclipse / Flash Builder. diff --git a/README.md b/README.md index fc855db..7e196bb 100644 --- a/README.md +++ b/README.md @@ -11,8 +11,8 @@ OPTIONS: -o: Path to the directory where processed data will be stored. This directory will be created if it doesn't exist. -k: Barcode kits to be used for barcoding. -m: medaka model for consensus polishing. --b: GPU memory control for medaka (optional) --v: Enable verbosity. +-b: GPU memory control for medaka (optional). +-v: Enable verbosity (optional). ``` ## Instructions to running fast5pipeline @@ -27,15 +27,15 @@ Before using this pipeline, you need to setup the required environment by instal ### Run fast5pipeline -To run this pipeline, kindly follow this instructions from your terminal: +To run this pipeline, kindly follow this instructions in your terminal from your home directory: ```bash # To get the pipeline source code on your laptop git clone https://github.com/AlbertRockG/fast5toGenome -# To add fast5pipeline to the PATH -cd fast5Genome/ -export PATH="$PWD:$PATH" +# To add fast5pipeline to the PATH if using bash shell +echo "export PATH=$PATH:$HOME/fast5Genome" >> .bashrc +source .bashrc # To activate the medaka environment, if using conda conda activate medaka