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diamond-software [2017/07/23 14:25]
aorth
diamond-software [2017/08/17 15:46]
aorth
Line 18: Line 18:
 <​code>​$ module load diamond/​0.9.9 <​code>​$ module load diamond/​0.9.9
 $ diamond</​code>​ $ diamond</​code>​
 +
 +An example SLURM submission script might look like:
 +
 +<​code>#​!/​bin/​env bash
 +#SBATCH -p batch
 +#SBATCH -n 4
 +#SBATCH -J diamond
 +
 +# Load diamond module
 +module load diamond/​0.9.9
 +
 +# Set up environment
 +export DATADIR=/​home/​aorth/​data
 +export WORKDIR=/​var/​scratch/​aorth/​diamond-2017-08-17
 +
 +# Create and change to working directory
 +mkdir -p $WORKDIR
 +cd $WORKDIR
 + 
 +diamond blastx -p 4 -q $DATADIR/​test_nt_seq.fa --sensitive -d /​export/​data/​bio/​diamond/​nr -o test_nt_seq.xml -f 5</​code>​
 +
 +Make sure to match the number of CPUs in your SLURM request (''​-n''​) with the amount in your diamond command line (''​-p''​).
  
 ===== Installation ====== ===== Installation ======
Line 28: Line 50:
 $ sudo cp diamond diamond_manual.pdf /​export/​apps/​diamond/​0.9.9</​code>​ $ sudo cp diamond diamond_manual.pdf /​export/​apps/​diamond/​0.9.9</​code>​
  
-Diamond requires specially formatted databases, which you create using ''​diamond makedb''​ subcommand. The input must be a FASTA file, but can be gzip compressed, for example the NR database from NCBI:+Diamond requires specially formatted databases, which you create using the ''​diamond makedb''​ subcommand. The input must be a FASTA file, but can be gzip compressed, for example the NR database from NCBI:
  
 <​code>​$ wget ftp://​ftp.ncbi.nlm.nih.gov/​blast/​db/​FASTA/​nr.gz <​code>​$ wget ftp://​ftp.ncbi.nlm.nih.gov/​blast/​db/​FASTA/​nr.gz
diamond-software.txt · Last modified: 2018/11/04 19:06 by aorth