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diamond-software [2016/11/23 16:12]
joguya created
diamond-software [2018/11/04 19:06] (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 16:12 by joguya