User Tools

Site Tools



This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
diamond-software [2017/07/23 06:52] aorthdiamond-software [2022/03/17 09:10] (current) aorth
Line 5: Line 5:
 ===== Information ===== ===== Information =====
-  * Latest Version: 0.9.9+  * Version: 2.0.14
   * Added: November, 2016   * Added: November, 2016
-  * Updated: July2017 +  * Updated: March2022 
-  * Link:  * Link:
 ===== Usage ===== ===== Usage =====
-See which versions of diamond are available:+See which versions are available:
 <code>$ module avail diamond</code> <code>$ module avail diamond</code>
-Load the diamond environment module and run it: +Load one version into your environment and run it: 
-<code>$ module load diamond/0.9.9+<code>$ module load diamond/2.0.14
 $ 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
 +diamond blastx -p 4 -q $DATADIR/test_nt_seq.fa --sensitive -d /export/data/bio/diamond/nr -o test_nt_seq.xml -f 5</code>
 +Make sure to match the number of CPUs in your SLURM request (''-n'') with the amount in your diamond command line (''-p'').
 ===== Installation ====== ===== Installation ======
Line 24: Line 46:
 <code>$ cd /tmp <code>$ cd /tmp
-$ wget$ wget 
 +$ sudo mkdir -p /export/apps/diamond/2.0.14/bin
 $ tar xf diamond-linux64.tar.gz $ tar xf diamond-linux64.tar.gz
-$ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.9.9</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 
 +$ 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