Requirements 

RattleSNP requires , and .

RattleSNP is developed to work mostly on an HPC distributed cluster but a local, single machine, installation is also possible.

Install RattleSNP PyPI package 

First, install the RattleSNP python package with pip.

python3 -m pip install rattleSNP
rattleSNP --help

Now, follow this documentation according to what you want, local or HPC mode.

Steps for LOCAL installation 

Install RattleSNP in a local (single machine) mode using rattleSNP install_local command line.

install_local 

Run installation for running in local computer.

The process downloading singularity images automatically.

rattleSNP install_local [OPTIONS]

Options

--bash_completion, --no-bash_completion

Allow bash completion of rattleSNP commands on the bashrc file

Default:: True

#:hide-header:

To create a pipeline, tools used by RattleSNP are wrapped into Singularity images. These images are automatically downloaded and used by the configuration files of the pipeline. Local mode install, without scheduler, is constrains to use these Singularity images.

the script uses the snakemake profiles to build the installation profile for rattleSNP. if –env is singularity, rattleSNP download images. Then, the script proposes to modify the following files to adapt to your system achitecture

Optionally (but recommended), after installing in local, you can check the RattleSNP installation using a dataset scaled for single machine. See the section Check install for details.

Steps for HPC distributed cluster installation 

RattleSNP uses any available snakemake profiles to ease cluster installation and resources management. Run the command rattleSNP install_cluster to install on a HPC cluster. We tried to make cluster installation as easy as possible, but it is somehow necessary to adapt a few files according to your cluster environment.

install_cluster 

Run installation of tool for HPC cluster

rattleSNP install_cluster [OPTIONS]

Options

-s, --scheduler <scheduler>

Type the HPC scheduler (for the moment, only slurm is available ! )

Default:: slurm
Options:: slurm

-e, --env <env>

Mode for tools dependencies

Default:: modules
Options:: modules | singularity

--bash_completion, --no-bash_completion

Allow bash completion of rattleSNP commands on the bashrc file

Default:: True

1. Adapt profile and cluster_config.yaml 

Now that RattleSNP is installed, it proposes default configuration files, but they can be modified. Please check and adapt these files to your own system architecture.

1. Adapt the pre-formatted f –env si`snakemake profile` to configure your cluster options. See the section 1. Snakemake profiles for details.

2. Adapt the cluster_config.yaml file to manage cluster resources such as partition, memory and threads available for each job. See the section 2. Adapting cluster_config.yaml for further details.

2. Adapt tools_path.yaml 

As RattleSNP uses many tools, you must install them using one of the two following possibilities:

Either through the containers,
Or using the module load mode,

rattleSNP install_cluster --help
rattleSNP install_cluster --scheduler slurm --env modules
# OR
rattleSNP install_cluster --scheduler slurm --env singularity

If --env singularity argument is specified, RattleSNP will download previously build Singularity images, containing the complete environment need to run RattleSNP (tools and dependencies).

Adapt the file :file:tools_path.yaml - in YAML (Yet Another Markup Language) - format to indicate RattleSNP where the different tools are installed on your cluster. See the section 3. How to configure tools_path.yaml for details.

Check install 

In order to test your install of RattleSNP, a data test called data_test_rattleSNP/ is available at http://nas-bgpi.myds.me/DOC/rattleSNP/data_test_rattleSNP.zip.

test_install 

Test_install function downloads a scaled data test, writes a configuration file adapted to it and proposes a command line already to run !!!

rattleSNP test_install [OPTIONS]

Options

-d, --data_dir <data_dir>: Required Path to download data test and create config.yaml to run test

This dataset will be automatically downloaded by RattleSNP in the -d repertory using :

rattleSNP test_install -d test

Launching the (suggested, to be adapted) command line in CLUSTER mode will perform the tests:

rattleSNP run_cluster --config test/data_test_config.yaml

In local mode, type :

rattleSNP run_local -t 8 -c test/data_test_config.yaml --singularity-args "--bind $HOME"

Advance installation 

1. Snakemake profiles 

The Snakemake-profiles project is an open effort to create configuration profiles allowing to execute Snakemake in various computing environments (job scheduling systems as Slurm, SGE, Grid middleware, or cloud computing), and available at https://github.com/Snakemake-Profiles/doc.

In order to run RattleSNP on HPC cluster, we take advantages of profiles.

Quickly, see here an example of the Snakemake SLURM profile we used for the French national bioinformatics infrastructure at IFB.

More info about profiles can be found here https://github.com/Snakemake-Profiles/slurm#quickstart.

Preparing the profile’s config.yaml file

Once your basic profile is created, to finalize it, modify as necessary the rattleSNP/rattleSNP/default_profile/config.yaml to customize Snakemake parameters that will be used internally by RattleSNP:

restart-times: 0
jobscript: "slurm-jobscript.sh"
cluster: "slurm-submit.py"
cluster-status: "slurm-status.py"
max-jobs-per-second: 1
max-status-checks-per-second: 10
local-cores: 1
jobs: 200                   # edit to limit the number of jobs submitted in parallel
latency-wait: 60000000
use-envmodules: true        # adapt True/False for env of singularuty, but only active one possibility !
use-singularity: false      # if False, please install all R packages listed in tools_config.yaml ENVMODULE/R
rerun-incomplete: true
printshellcmds: true

2. Adapting cluster_config.yaml

In the cluster_config.yaml file, you can manage HPC resources, choosing partition, memory and threads to be used by default, or specifically, for each rule/tool depending on your HPC Job Scheduler (see there). This file generally belongs to a Snakemake profile (see above).

Warning

If more memory or threads are requested, please adapt the content of this file before running on your cluster.

A list of RattleSNP rules names can be found in the section Threading rules inside RattleSNP

Warning

For some rules in the cluster_config.yaml as rule_graph or run_get_versions, we use by default wildcards, please don’t remove it.

3. How to configure tools_path.yaml 

In the tools_path file, you can find two sections: SINGULARITY and ENVMODULES. In order to fill it correctly, you have 2 options:

1. Use only SINGULARITY containers: in this case, fill only this section. Put the path to the built Singularity images you want to use. Absolute paths are strongly recommended. See the section ‘How to build singularity images’ for further details.

SINGULARITY:
    REPORT : 'INSTALL_PATH/containers/Singularity.report.sif'
    TOOLS : 'INSTALL_PATH/containers/Singularity.rattleSNP_tools.sif'

Warning

To ensure SINGULARITY containers to be really used, one needs to make sure that the –use-singularity flag is included in the snakemake command line.

Use only ENVMODULES: in this case, fill this section with the modules available on your cluster (here is an example):

MODULES:
    "SAMTOOLS": "samtools"                  # use for filter reads and convert sam to bam
    "PYTHON3": "python"                    # Python3 >=3.6 with require libraries
    "BWA": "bwa"                         # for make the mapping
    "ATROPOS": "python"                    # for call atropos
    "FASTQC": "fastqc"                   # for control quality
    "PICARDTOOLS": "picard"         # for control quality
    "GATK4": "gatk4"                     # for control quality
    "BCFTOOLS": "bcftools"                  # for contact vcf

RattleSNP needs a wide set of R modules for reporting. If you use ENVMODULE R, just have a look at dependencies in the Containers/Singularity.report.def file. Yes, plenty of packages!! That’s why we provide build Singularity containers ready to use and recommend them for the R part.

Note

TIP !! We provide a Singularity container for all R packages (Singularity.report.def), thus you can use this one to create a dedicated module environment.

Warning

Make sure to specify the –use-envmodules flag in the snakemake command line for ENVMODULE to be implemented. More details can be found here: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#using-environment-modules

And more …

How to build Singularity images

You can build your own image using the available .def recipes from the rattleSNP/rattleSNP/containers/ directory.

Warning

Be careful, you need root access to build Singularity images

cd rattleSNP/rattleSNP/containers/
sudo make build

Threading rules inside RattleSNP

Please find here the rules names found in RattleSNP code. It is recommended to set threads using the snakemake command when running on a single machine, or in a cluster configuration file to manage cluster resources through the job scheduler. This would save users a painful exploration of the snakefiles of RattleSNP.

bwa_index
run_atropos
run_fastqc
bwa_mem_sort_bam
run_bwa_aln
bwa_sampe_sort_bam
samtools_index
samtools_idxstats
merge_idxstats
samtools_depth
bam_stats_to_csv
merge_bam_stats
report
picardTools_mark_duplicates
create_sequence_dict
create_sequence_fai
gatk_HaplotypeCaller
gatk_GenomicsDBImport
gatk_GenotypeGVCFs_merge
bcftools_concat
vcftools_filter
vcf_to_fasta
vcf_to_geno
vcf_stats
report_vcf
run_raxml
run_raxml_ng