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--- diamond-software [2016/11/23 13:12] – created joguya
+++ diamond-software [2022/03/17 09:10] (current) – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Latest Version: 0.8.27
+  * Version: 2.0.14
   * Added: November, 2016
-  * Link: http://ab.inf.uni-tuebingen.de/software/diamond/
+  * Updated: March, 2022
+  * Link: https://github.com/bbuchfink/diamond
 ===== Usage =====
-See which versions of diamond are available:
+See which versions are available:
-<code>$ module avail diamond
+<code>$ module avail diamond</code>
-</code>
-Load diamond
+Load one version into your environment and run it:
-<code>$ module load diamond/0.8.27</code>
+<code>$ module load diamond/2.0.14
+$ 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 $DATADIR/test_nt_seq.fa --sensitive -d /export/data/bio/diamond/nr -o test_nt_seq.xml -f 5</code>
+Make sure to match the number of CPUs in your SLURM request (''-n'') with the amount in your diamond command line (''-p'').
 ===== Installation ======
-Notes from the sysadmin during installation:<code>
+Notes from the sysadmin during installation:
-$ cd /tmp/
-$ wget https://github.com/bbuchfink/diamond/releases/download/v0.8.27/diamond-linux64.tar.gz
+<code>$ cd /tmp
-$ tar -xvf diamond-linux64.tar.gz
+$ wget http://github.com/bbuchfink/diamond/releases/download/v2.0.14/diamond-linux64.tar.gz
-$ sudo mkdir -p /export/apps/diamond/0.8.27/
+$ sudo mkdir -p /export/apps/diamond/2.0.14/bin
-$ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.8.27/
+$ tar xf diamond-linux64.tar.gz
-</code>
+$ sudo cp diamond /export/apps/diamond/2.0.14/bin</code>
+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
+$ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz
+$ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
+$ unzip taxdmp.zip
+$ diamond makedb --in nr.gz --db nr --taxonmap prot.accession2taxid.FULL.gz --taxonnodes nodes.dmp --taxonnames names.dmp
+$ sudo mkdir -p /export/data/bio/diamond
+$ sudo cp nr.dmnd /export/data/bio/diamond</code>