diamond-software
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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: |
* Added: November, 2016 | * Added: November, 2016 | ||
- | * Updated: | + | * Updated: |
- | * Link: http://ab.inf.uni-tuebingen.de/software/diamond/ | + | * Link: https://github.com/bbuchfink/diamond |
| | ||
===== Usage ===== | ===== Usage ===== | ||
- | See which versions | + | See which versions are available: |
< | < | ||
- | Load the diamond | + | Load one version into your environment and run it: |
- | < | + | < |
$ diamond</ | $ diamond</ | ||
+ | |||
+ | An example SLURM submission script might look like: | ||
+ | |||
+ | < | ||
+ | #SBATCH -p batch | ||
+ | #SBATCH -n 4 | ||
+ | #SBATCH -J diamond | ||
+ | |||
+ | # Load diamond module | ||
+ | module load diamond/ | ||
+ | |||
+ | # 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 ====== | ||
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< | < | ||
- | $ wget https:// | + | $ wget http:// |
+ | $ sudo mkdir -p / | ||
$ tar xf diamond-linux64.tar.gz | $ tar xf diamond-linux64.tar.gz | ||
- | $ sudo cp diamond | + | $ sudo cp diamond / |
- | ===== Create Databases ===== | + | Diamond requires specially formatted databases, which you create using the '' |
- | Diamond requires specially formatted databases, which you create using '' | + | |
< | < | ||
- | $ diamond makedb --in nr.gz -d nr | + | $ wget ftp:// |
+ | $ 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 mkdir -p / | ||
$ sudo cp nr.dmnd / | $ sudo cp nr.dmnd / |
diamond-software.1500808462.txt.gz · Last modified: 2017/07/23 11:14 by aorth