diff --git a/README.md b/README.md index a7116423f02a34dc4fa0e815f3ee98cadb00ca48..f229a8cc29d6634bc8d4d78fcef04ee05cb53bbc 100644 --- a/README.md +++ b/README.md @@ -12,14 +12,12 @@ This was designed to process RADseq data from [RESERVEBENEFIT](https://www.biodi 1. [Prerequisite](#21-prerequisite) 2. [Data Files](#22-data-files) 3. [Set up](#23-set-up) -3. [Reporting bugs](#4-reporting-bugs) +3. [Reporting bugs](#3-reporting-bugs) 4. [Running the pipeline](#5-running-the-pipeline) - 1. [Filter raw data](#51-filter-raw-data) - 2. [Georeferenced sequences alignments by species](#52-data-files) - 3. [Species sequence pairwise comparison](#53-species-sequence-pairwise-comparison) - 4. [Genetic Diversity calculation](#54-genetic-diversity-calculation) - 5. [Statistical analysis](#55-statistical-analysis) - + 1. [Initialisation](#41-initialisation) + 2. [Configuration](#42-configuration) + 3. [Run the pipeline into a single command](#43-run-the-pipeline-into-a-single-command) + 4. [Run the pipeline step by step](#44-run-the-pipeline-step-by-step) # 1. Introduction @@ -34,64 +32,70 @@ blablabla You must install the following softwares and packages : - [SNAKEMAKE 5.3.0](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) -Check version and if the program is correctly installed by typing : -``` -snakemake --version -## should give you the output -5.3.0 -``` + * Check version and if the program is correctly installed by typing : + + ``` + snakemake --version + ## should give you the output + 5.3.0 + ``` - [STACKS 2.0b](http://catchenlab.life.illinois.edu/stacks/) -Check version and if programs are correctly installed by typing : -``` -process_radtags --version -clone_filter --version -gstacks --version -populations --version -## should give you the output -2.0b -``` + * Check version and if programs are correctly installed by typing : + + ``` + process_radtags --version + clone_filter --version + gstacks --version + populations --version + ## should give you the output + 2.0b + ``` - [BWA 0.7.17](https://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial) -Download `bwa` at: http://sourceforge.net/projects/bio-bwa/files/ -``` -tar -xvf bwa-x.x.x.tar.bz2 -cd bwa-x.x.x -./configure --prefix=/where/to/install -make -make install -``` -Check version and if programs are correctly installed by typing : -``` -bwa -## should give you the output -Program: bwa (alignment via Burrows-Wheeler transformation) -Version: 0.7.17-r1188 -... -``` -- [SAMTOOLS](http://www.htslib.org/) -Download `htslib` and `samtools` at : http://www.htslib.org/download/ -Building each desired package from source is very simple: -``` -cd htslib-1.x -./configure --prefix=/where/to/install -make -make install -cd .. -## and similarly for samtools : -cd samtools-1.x -./configure --prefix=/where/to/install -make -make install -``` -Check version and if programs are correctly installed by typing : -``` -samtools --version -## should give you the output -samtools 1.9 -Using htslib 1.9 -Copyright (C) 2018 Genome Research Ltd. -``` + * Download `bwa` at: http://sourceforge.net/projects/bio-bwa/files/ + + ``` + tar -xvf bwa-x.x.x.tar.bz2 + cd bwa-x.x.x + ./configure --prefix=/where/to/install + make + make install + ``` + * Check version and if programs are correctly installed by typing : + + ``` + bwa + ## should give you the output + Program: bwa (alignment via Burrows-Wheeler transformation) + Version: 0.7.17-r1188 + ... + ``` +- [SAMTOOLS 1.9 ](http://www.htslib.org/) + * Download `htslib` and `samtools` at : http://www.htslib.org/download/ + * Building each desired package from source is very simple: + + ``` + cd htslib-1.x + ./configure --prefix=/where/to/install + make + make install + cd .. + ## and similarly for samtools : + cd samtools-1.x + ./configure --prefix=/where/to/install + make + make install + ``` + * Check version and if programs are correctly installed by typing : + + ``` + samtools --version + ## should give you the output + samtools 1.9 + Using htslib 1.9 + Copyright (C) 2018 Genome Research Ltd. + ``` ## 2.2 Data Files The included data files are : @@ -105,24 +109,27 @@ The included data files are : clone the project and switch to the main folder, it's your working directory ``` -git clone dzdzdzworldmap_fish_genetic_diversity.git +git clone http://gitlab.mbb.univ-montp2.fr/reservebenefit/snakemake_stacks2.git cd snakemake_stacks2 ``` +You will see the following folders : + + -# 4. Reporting bugs +# 3. Reporting bugs If you're sure you've found a bug — e.g. if one of my programs crashes with an obscur error message, or if the resulting file is missing part of the original data, then by all means submit a bug report. -I use [GitLab's issue system](https://gitlab.com/reservebenefit/worldmap_fish_genetic_diversity/issues) +I use [GitLab's issue system](https://gitlab.com/reservebenefit/snakemake_stacks2/issues) as my bug database. You can submit your bug reports there. Please be as verbose as possible — e.g. include the command line, etc # 4. Running the pipeline -Quickstart +## 4.1 Initialisation * open a shell * make a folder, name it yourself, I named it workdir @@ -134,10 +141,27 @@ cd workdir * clone the project and switch to the main folder, it's your working directory ``` -git clone +git clone http://gitlab.mbb.univ-montp2.fr/reservebenefit/snakemake_stacks2.git cd snakemake_stacks2 ``` +## 4.2 Configuration +WORK IN PROGRESS !!!! + +## 4.3 Run the pipeline into a single command +Once you finished [Initialisation](#41-initialisation) and [Configuration](#42-configuration) steps. You can run the whole pipeline simply typing : +``` +## number of CPU cores available for running the pipeline (for instance here 64 cores) +N_CORES=64 +## run the pipeline into a single command +bash main.sh $N_CORES +``` + + +## 4.4 Run the pipeline step by step WORK IN PROGRESS !!!! that's it ! The pipeline is running and crunching your data. Look for the log folder output folder after the pipeline is finished. + + +