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Commit 19343e4f authored by Sarah Maman-Haddad's avatar Sarah Maman-Haddad
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(minor) Complete binaries list to precise in the config_calling.yaml file. Binaries or conda mamba

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......@@ -130,19 +130,38 @@ Finally, this VCF file will be splitted into two VCF files for SNP or INDEL usin
## 3. Dependencies
The workflow depends on:
###3.1. Links to binaries
The workflow depends on: LIST TO CHECK !
* cutadapt
* trimgalore (version 0.4.5)
* STAR (version 2.5.2b)
* picard.jar (version 2.1.1)
* samtools (version 1.3.1 )
* rsem-prepare-reference ( RSEM version 1.3.0)
* rsem-calculate-expression ( RSEM version 1.3.0)
* rsem-prepare-reference (RSEM version 1.3.0)
* rsem-calculate-expression (RSEM version 1.3.0)
* GenomeAnalysisTK.jar (version 3.7)
* java (version 8)
* snakemake (version 4.8.0)
* maskFastaFromBed (bedtools version 2.26.0)
* vcf-merge (VCFtools version 0.1.15)
* bgzip (Tabix version 0.2.5)
* tabix (Tabix version 0.2.5)
* python3.6.3 (version 3.6.3)
* fastqc (version 0.11.7)
Theses softwares need to be available in you PATH or in a bin directory precised in the config.yaml file with the bin_dir option.
###3.2. Using conda mamba
```
conda activate mamba
mamba create -n env_name -c bioconda -c conda-forge cutadapt trim-galore star samtools gatk4 rsem
conda activate /path/to/miniconda/envs/mamba/envs/env_name
module load system/Python-3.6.3
export PERL5LIB=""
```
## 4. Configure and running workflow
......
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