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diamond-software
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diamond-software [2016/11/23 13:12] joguya created |
diamond-software [2018/11/04 16:06] aorth |
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| ===== Information ===== | ===== Information ===== | ||
| - | * Latest | + | * Version: 0.9.9 |
| * Added: November, 2016 | * Added: November, 2016 | ||
| + | * Updated: July, 2017 | ||
| * Link: http:// | * Link: http:// | ||
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| Line 12: | Line 13: | ||
| See which versions of diamond are available: | See which versions of diamond are available: | ||
| - | < | + | < |
| - | </ | + | |
| - | Load diamond | + | Load the 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 ====== | ||
| - | Notes from the sysadmin during installation:< | + | Notes from the sysadmin during installation: |
| - | $ cd /tmp/ | + | |
| - | $ wget https:// | + | < |
| - | $ tar -xvf diamond-linux64.tar.gz | + | $ wget https:// |
| - | $ sudo mkdir -p / | + | $ tar xf diamond-linux64.tar.gz |
| - | $ sudo cp diamond | + | $ sudo cp diamond diamond_manual.pdf |
| - | </ | + | |
| + | Diamond requires specially formatted databases, which you create using the '' | ||
| + | |||
| + | < | ||
| + | $ diamond makedb --in nr.gz -d nr | ||
| + | $ sudo mkdir -p /export/ | ||
| + | $ sudo cp nr.dmnd / | ||
diamond-software.txt · Last modified: 2018/11/04 16:06 by aorth
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