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diamond-software [2016/11/23 13:12]
joguya created
diamond-software [2018/11/04 16:06] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Latest Version: 0.8.27+  * Version: 0.9.9
   * Added: November, 2016   * Added: November, 2016
 +  * Updated: July, 2017
   * Link: http://ab.inf.uni-tuebingen.de/software/diamond/   * Link: http://ab.inf.uni-tuebingen.de/software/diamond/
      
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 See which versions of diamond are available: See which versions of diamond are available:
-<code>$ module avail diamond +<code>$ module avail diamond</code>
-</code>+
  
-Load diamond +Load the diamond environment module and run it: 
-<code>$ module load diamond/0.8.27</code>+<code>$ module load diamond/0.9.
 +$ 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 ====== ===== 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 https://github.com/bbuchfink/diamond/releases/download/v0.9.9/diamond-linux64.tar.gz 
-$ sudo mkdir -p /export/apps/diamond/0.8.27+$ tar xf diamond-linux64.tar.gz 
-$ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.8.27+$ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.9.9</code> 
-</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 ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz 
 +$ diamond makedb --in nr.gz -d nr 
 +$ sudo mkdir -p /export/data/bio/diamond 
 +$ sudo cp nr.dmnd /export/data/bio/diamond</code>
diamond-software.1479906757.txt.gz · Last modified: 2016/11/23 13:12 by joguya