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diamond-software [2016/11/23 13:12] – created joguyadiamond-software [2022/03/17 09:10] (current) aorth
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 ===== Information ===== ===== Information =====
-  * Latest Version: 0.8.27+  * Version: 2.0.14
   * Added: November, 2016   * Added: November, 2016
-  * Link:  * Updated: March, 2022 
 +  * Link:
 ===== Usage ===== ===== Usage =====
-See which versions of diamond are available: +See which versions are available: 
-<code>$ module avail diamond +<code>$ module avail diamond</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 $DATADIR/test_nt_seq.fa --sensitive -d /export/data/bio/diamond/nr -o test_nt_seq.xml -f 5</code> 
 +Make sure to match the number of CPUs in your SLURM request (''-n'') with the amount in your diamond command line (''-p'').
 ===== Installation ====== ===== Installation ======
-Notes from the sysadmin during installation:<code> +Notes from the sysadmin during installation: 
-$ cd /tmp/ + 
-$ wget +<code>$ cd /tmp 
-tar -xvf diamond-linux64.tar.gz +$ wget 
-$ 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'' subcommandThe input must be a FASTA file, but can be gzip compressed, for example the NR database from NCBI: 
 +<code>$ wget 
 +$ wget 
 +$ unzip 
 +$ 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>
diamond-software.txt · Last modified: 2022/03/17 09:10 by aorth