diff --git a/docs/source/install.md b/docs/source/install.md index bfb67f67de5350b12ba5ea87fb4caae25ddf6a20..cc75972da507b6b9841abd1b7d60c35b10e67077 100644 --- a/docs/source/install.md +++ b/docs/source/install.md @@ -7,34 +7,8 @@ $ git clone https://forgemia.inra.fr/umr-gdec/magatt.git ``` -## Dependencies - Conda - -We recommend to build the environment using conda (developped with miniconda 3, conda 4.9.2 ) with the file [environment.yml](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/envs/environment.yml): - -```console -$ conda env create -f envs/environment.yml -n magatt -``` - -Once created, you can activate the environment with: - -```console -$ conda activate magatt -``` - -All the dependancies installed in the conda env are listed below. +## Dependencies - Snakemake * Snakemake : >=5.5.2 -* Python: 3.5 -* Biopython: 1.68 -* numpy: 1.15 -* pandas: 0.23 -* pysam: 0.15 -* Bedtools: 2.27 -* Blat: 36 -* Exonerate (fastavalidcds): 2.4.0 -* GenomeTools: 1.5.9 -* gffread: 0.9.11 -* GMAP: 2018-05-11 -* NCBI-blast (BLAST+): 2.6 -* Samtools: 1.9 -* BWA: 0.7 + +All the dependancies are installed in a docker image : https://hub.docker.com/r/helrim/magatt used by default by MAGATT \ No newline at end of file