diamond-software
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diamond-software [2016/11/23 13:12] – created joguya | diamond-software [2022/03/17 09:10] (current) – aorth | ||
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===== Information ===== | ===== Information ===== | ||
- | * Latest | + | * Version: |
* Added: November, 2016 | * Added: November, 2016 | ||
- | * Link: http://ab.inf.uni-tuebingen.de/software/diamond/ | + | |
+ | | ||
| | ||
===== Usage ===== | ===== Usage ===== | ||
- | See which versions | + | See which versions are available: |
- | < | + | < |
- | </ | + | |
- | Load diamond | + | Load one version into your environment and run it: |
- | < | + | < |
+ | $ diamond</ | ||
+ | |||
+ | An example SLURM submission script might look like: | ||
+ | |||
+ | < | ||
+ | #SBATCH -p batch | ||
+ | #SBATCH -n 4 | ||
+ | #SBATCH -J diamond | ||
+ | |||
+ | # Load diamond module | ||
+ | module load diamond/0.9.9 | ||
+ | |||
+ | # Set up environment | ||
+ | export DATADIR=/ | ||
+ | export WORKDIR=/ | ||
+ | |||
+ | # Create and change to working directory | ||
+ | mkdir -p $WORKDIR | ||
+ | cd $WORKDIR | ||
+ | |||
+ | diamond blastx -p 4 -q $DATADIR/ | ||
+ | |||
+ | Make sure to match the number of CPUs in your SLURM request ('' | ||
===== Installation ====== | ===== Installation ====== | ||
- | Notes from the sysadmin during installation:< | + | Notes from the sysadmin during installation: |
- | $ cd /tmp/ | + | |
- | $ wget https:// | + | < |
- | $ tar -xvf diamond-linux64.tar.gz | + | $ wget http:// |
- | $ sudo mkdir -p / | + | $ sudo mkdir -p / |
- | $ sudo cp diamond diamond_manual.pdf /export/apps/diamond/0.8.27/ | + | $ tar xf diamond-linux64.tar.gz |
- | </ | + | $ sudo cp diamond |
+ | |||
+ | Diamond requires specially formatted databases, which you create using the '' | ||
+ | |||
+ | < | ||
+ | $ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz | ||
+ | $ wget ftp:// | ||
+ | $ unzip taxdmp.zip | ||
+ | $ diamond makedb --in nr.gz --db nr --taxonmap prot.accession2taxid.FULL.gz --taxonnodes nodes.dmp --taxonnames names.dmp | ||
+ | $ sudo mkdir -p / | ||
+ | $ sudo cp nr.dmnd / |
diamond-software.1479906757.txt.gz · Last modified: 2016/11/23 13:12 by joguya