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GOMAP-singularity Boilerplate

The GOMAP-singularity Boilerplate repo has been distributed for the use with GOMAP-singularity to annotate GO terms to plant genes on SLURM high-performance computing environments.

Obtaining the boilerplate

git clone https://github.com/Dill-PICL/GOMAP-boilerplate.git /path/for/annotation

GOMAP-singularity steps

GOMAP-singularity has seven steps for annotating the proteins. Some of these steps are parallelized and some of them are not parallelized.

Number Step Single MPI Concurrent
1 seqsim Y N Y
2 domain Y Y Y
3 fanngo Y N Y
4 mixmeth-blast Y Y Y
5 mixmeth-preproc Y N N
6 mixmeth Y N N
7 aggregate Y N N

Customizing files for the cluster

The boilerplate has steps to run the annotation on Sorghum reference genome, and the input file is Sbicolor_454_v3.1.1.protein_primaryTranscriptOnly.fa. Files have to be customized for individual clusters

Edit the config.yaml file

input:
  #input fasta file name
  fasta: your_input.fasta
  # output file basename
  basename: desired_output_basename
  #input NCBI taxonomy id
  taxon: "XXXXX"
  # Name of the species
  species: "You species"
  # Email is mandatory
  email: [email protected]
  #Number of CPUs used for tools
  cpus: Find this out from the cluster help page
  #Whether mpi should be used (mpich-3.2.1  is default)
  mpi: True
  #what the name of the 
  tmpdir: "/tmpdir"

Edit the setenv.sh file

# set the tmpdir to a variable that will be local to the specific node
export tmpdir="$LOCAL" # or other location based on cluster

# Loading necessary modules and this would be specific to each cluster

# Loading the mpich module. This is based on how it is called on the cluster and contact the cluster help to get the correct module to load
module load mpich

# Load the singulairy module. GOMAP-singulrity currently only works with Singulairty 2.6.
x and you have to use the correct version
module load singularity/3.1.x

#Set the location of GOMAP-singularity base directory. This is essential to correctly run the pipeline
export GOMAP_LOC="/path/to/GOMAP-singularity/"

Edit the *.job files

Each cluster has specific parameters that need to be optimized for the sbatch files before they can be successfully run. A list of such parameters are given below.

  1. --ntasks-per-node=XX This parameter is used by some clusters to assign entire nodes so assign the number based on the number of cores available on each compute node

  2. --nodes=XX This parameter is used for assigning number of nodes for each job. The domain and mixmeth-blast jobs need customization based on the number of nodes you can use for parallelized jobs

  3. --partition=XX Some of the clusters have specific partitions that have to be used for big or parallelized jobs so find out which partition can be used for that

  4. -mail-user=[email protected] Assign a correct value to get job status changes to see which jobs are done.