Differences

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--- diamond-software [2017/07/23 11:14] – aorth
+++ diamond-software [2017/08/17 12:46] – aorth
@@ Line 18: / Line 18: @@
 <code>$ module load diamond/0.9.9
 $ 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 ======
@@ Line 28: / Line 50: @@
 $ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.9.9</code>
-===== Create Databases =====
+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:
-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:
 <code>$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz