snakevir

Documentation : https://snakevir.readthedocs.io/en/latest/

snakevir [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

edit_cluster

The command make_config is used for create config fime at yaml format for snakevir. You have 2 choice, you can use arguement for write all information needed in config or you can only use some argument (-o is mandatory) and wirte in the file after the missing information.

snakevir edit_cluster [OPTIONS]

Options

-p, --partition <partition>

Name of the default partition.

-a, --account <account>

Name of you’re account for launch job in cluster

-e, --edit

Edit cluster config for less/more ressources

install_cluster

This function allow to install tools with conda and dowload database needed by snakevir except nt & nr database

snakevir install_cluster [OPTIONS]

Options

-p, --path <path>

Required Give the installation PATH for conda environment that contains all the necessary tools for snakevir.

-s, --skip

Skip all install and download if it’s already existing

-t, --tool

Update conda environment (Re-install conda environment even if it’s already install)

-d, --database

Update database (Re-download files even if it’s already download)

make_config

The command make_config is used for create config fime at yaml format for snakevir. You have 2 choice, you can use arguement for write all information needed in config or you can only use some argument (-o is mandatory) and wirte in the file after the missing information.

snakevir make_config [OPTIONS]

Options

-o, --output <output>

Required Path of the output file with ‘.yaml’ extension (config.yml needed for snakevir.

-d, --output_directory <output_directory>

Path of the output directory for Snakevir’s result.

-n, --name <name>

Name of run (ex : HNXXXXXX)

-f, --fastq <fastq>

Path to the fastq directory

-g, --host_genome <host_genome>

Path to the genome host at fasta format

--r1 <r1>

Type of your R1 fastq files contains in FASTQ directory (for exemple : ‘_R1’ or ‘_1’, etc. )

Default:

_1

--r2 <r2>

Type of your R2 fastq files contains in FASTQ directory (for exemple : ‘_R2’ or ‘_2’, etc. )

Default:

_2

--ext <ext>

Etension of your reads files in the FASTQ directory (for exemple : ‘.fastq.gz’ or ‘.fq’, etc.)

Default:

.fastq.gz

--path_diamond_nr <path_diamond_nr>

Path to the diamond nr database

--path_blast_nt <path_blast_nt>

Path to the blast nt database

--A3 <a3>

Sequence of Adapter in 3’

Default:

CAGCGGACGCCTATGTGATG

--A5 <a5>

Sequence of Adapter in 5’

Default:

CATCACATAGGCGTCCGCTG