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spades-software
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| Both sides previous revision Previous revision Next revision | Previous revision | ||
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spades-software [2016/08/16 05:15] joguya |
spades-software [2019/10/04 12:58] (current) aorth |
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| ===== Information ===== | ===== Information ===== | ||
| - | * Version: 3.6.1 | + | * Version: 3.13.0 |
| * Added: September, 2014 | * Added: September, 2014 | ||
| - | * Updated: | + | * Updated: |
| - | * Link: http://bioinf.spbau.ru/spades | + | * Link: https://github.com/ablab/spades |
| ===== Usage ===== | ===== Usage ===== | ||
| Line 13: | Line 13: | ||
| See versions of spades which are available: | See versions of spades which are available: | ||
| < | < | ||
| + | |||
| + | Load one version into your environment and run it: | ||
| + | < | ||
| + | $ spades.py --help</ | ||
| === Example batch job === | === Example batch job === | ||
| Line 21: | Line 25: | ||
| #SBATCH -J spades | #SBATCH -J spades | ||
| - | module load spades/3.6.1 | + | module load spades/3.13.0 |
| readonly DATADIR=~/ | readonly DATADIR=~/ | ||
| Line 41: | Line 45: | ||
| Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
| - | < | + | < |
| - | $ cd /tmp | + | $ wget https://github.com/ablab/ |
| - | $ wget http://spades.bioinf.spbau.ru/release3.6.1/SPAdes-3.6.1.tar.gz | + | $ tar xf SPAdes-3.13.0.tar.gz |
| - | $ tar xf SPAdes-3.6.1.tar.gz | + | $ cd SPAdes-3.13.0 |
| - | $ cd SPAdes-3.6.1 | + | $ sudo mkdir / |
| - | $ scl enable devtoolset-2 bash | + | $ sudo chown aorth / |
| - | $ sudo mkdir -p / | + | $ sudo yum install centos-release-scl cmake |
| - | $ sudo chown joguya: | + | $ sudo yum install devtoolset-6-gcc.x86_64 devtoolset-6-gcc-c++.x86_64 |
| - | $ sudo chown -R root:root / | + | $ PREFIX=/export/ |
| - | + | $ sudo chown -R root:root / | |
| - | ===== Running ===== | + | |
| - | After loading the module, consult the built-in help: | + | |
| - | < | + | Note: if you get the error '' |
spades-software.1471324557.txt.gz · Last modified: 2016/08/16 05:15 by joguya
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