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diamond-software [2017/07/23 11:14]
aorth
diamond-software [2022/03/17 09:10] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Latest Version: 0.9.9+  * Version: 2.0.14
   * Added: November, 2016   * Added: November, 2016
-  * Updated: July2017 +  * Updated: March2022 
-  * Link: http://ab.inf.uni-tuebingen.de/software/diamond/+  * Link: https://github.com/bbuchfink/diamond
      
 ===== 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
 +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 ======
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://github.com/bbuchfink/diamond/releases/download/v0.9.9/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/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>
  
-===== 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 <code>$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
-$ diamond makedb --in nr.gz -nr+$ 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 mkdir -p /export/data/bio/diamond
 $ sudo cp nr.dmnd /export/data/bio/diamond</code> $ sudo cp nr.dmnd /export/data/bio/diamond</code>
diamond-software.1500808462.txt.gz · Last modified: 2017/07/23 11:14 by aorth