spades-software
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spades-software [2016/08/15 13:30] – [Information] joguya | spades-software [2022/09/20 07:38] (current) – aorth | ||
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===== Information ===== | ===== Information ===== | ||
- | * Version: 3.6.0 | + | * Version: 3.15 (3.15.5) |
* Added: September, 2014 | * Added: September, 2014 | ||
- | * Updated: | + | * Updated: |
- | * Link: http://bioinf.spbau.ru/spades | + | * Link: https://github.com/ablab/spades |
===== Usage ===== | ===== Usage ===== | ||
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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 | ||
+ | $ spades.py --test</ | ||
=== Example batch job === | === Example batch job === | ||
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#SBATCH -J spades | #SBATCH -J spades | ||
- | module load spades/3.6.0 | + | module load spades/3.13.0 |
readonly DATADIR=~/ | readonly DATADIR=~/ | ||
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echo | echo | ||
- | echo " | + | echo " |
echo | echo | ||
echo " | echo " | ||
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Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
- | < | + | < |
- | $ cd /tmp | + | $ wget https:// |
- | $ wget http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz | + | $ tar xf SPAdes-3.15.5-Linux.tar.gz |
- | $ tar xf SPAdes-3.5.0.tar.gz | + | $ sudo mv / |
- | $ cd SPAdes-3.5.0 | + | $ sed -i '1s/python/python3/' SPAdes-3.15.5-Linux/bin/spades.py |
- | $ scl enable devtoolset-2 bash | + | $ sudo cp -r SPAdes-3.15.5-Linux / |
- | $ sudo mkdir -p / | + | |
- | $ sudo chown aorth: | + | |
- | $ PREFIX=/export/apps/spades/3.5.0 ./spades_compile.sh | + | |
- | $ sudo chown -R root: | + | |
- | + | ||
- | ===== Running ===== | + | |
- | After loading the module, consult the built-in help: | + | |
- | < | + | Note: if you get the error '' |
spades-software.1471267803.txt.gz · Last modified: 2016/08/15 13:30 by joguya