spades-software
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spades-software [2014/09/22 16:01] – created aorth | spades-software [2022/02/21 17:48] – aorth | ||
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- | ====== | + | ====== |
+ | SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. | ||
===== Information ===== | ===== Information ===== | ||
- | * Version: 3.1.1 | + | * Version: 3.15 (3.15.4) |
* Added: September, 2014 | * Added: September, 2014 | ||
- | * Link: http://bioinf.spbau.ru/spades | + | |
+ | | ||
===== Usage ===== | ===== Usage ===== | ||
- | === 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 === | ||
+ | |||
+ | < | ||
+ | #SBATCH -p highmem | ||
+ | #SBATCH -n 8 | ||
+ | #SBATCH -J spades | ||
+ | |||
+ | module | ||
+ | |||
+ | readonly DATADIR=~/ | ||
+ | readonly OUTDIR=/ | ||
+ | |||
+ | # create output directory | ||
+ | mkdir -p ${OUTDIR} | ||
+ | |||
+ | # run spades with 8 CPUs on mammoth (it has 16 logical CPUs, but only 8 are physical) | ||
+ | # run spades with 384 GB of RAM (default is 250, but it ran out of memory before) | ||
+ | spades.py -k 27 -1 ${DATADIR}/ | ||
+ | |||
+ | echo | ||
+ | echo " | ||
+ | echo | ||
+ | echo " | ||
===== Installation ====== | ===== Installation ====== | ||
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/release3.1.1/SPAdes-3.1.1.tar.gz | + | $ tar xf SPAdes-3.15.4.tar.gz |
- | cd SPAdes-3.1.1 | + | $ cd SPAdes-3.15.4 |
- | sed -i ' | + | $ sudo chown aorth / |
- | scl enable devtoolset-1.1 bash | + | $ sudo mkdir -p / |
- | sudo mkdir -p / | + | $ scl enable devtoolset-7 bash |
- | sudo chown aorth: | + | $ module load python/3.9 |
- | PREFIX=/ | + | $ sed -i ' |
- | sudo chown -R root:root / | + | $ PREFIX=/ |
+ | $ sudo chown -R root:root / | ||
+ | |||
+ | Note: if you get the error '' |
spades-software.txt · Last modified: 2022/09/20 07:38 by aorth