spades-software
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
spades-software [2017/12/25 20:46] – aorth | spades-software [2025/05/30 07:39] (current) – aorth | ||
---|---|---|---|
Line 4: | Line 4: | ||
===== Information ===== | ===== Information ===== | ||
- | * Version: | + | * Version: |
* Added: September, 2014 | * Added: September, 2014 | ||
- | * Updated: | + | * Updated: |
- | * Link: http://cab.spbu.ru/software/spades/ | + | * Link: https://github.com/ablab/spades |
===== Usage ===== | ===== Usage ===== | ||
- | See versions | + | See versions which are available: |
< | < | ||
- | After loading the module, consult the built-in help: | + | Load one version into your environment and run it: |
- | < | + | < |
+ | $ spades.py --help | ||
+ | $ spades.py --test</ | ||
=== Example batch job === | === Example batch job === | ||
Line 24: | Line 26: | ||
#SBATCH -J spades | #SBATCH -J spades | ||
- | module load spades/3.6.1 | + | module load spades/3.15 |
readonly DATADIR=~/ | readonly DATADIR=~/ | ||
Line 32: | Line 34: | ||
mkdir -p ${OUTDIR} | mkdir -p ${OUTDIR} | ||
- | # run spades with 8 CPUs on mammoth (it has 16 logical CPUs, but only 8 are physical) | + | # run spades with 8 CPU threads |
# run spades with 384 GB of RAM (default is 250, but it ran out of memory before) | # run spades with 384 GB of RAM (default is 250, but it ran out of memory before) | ||
spades.py -k 27 -1 ${DATADIR}/ | spades.py -k 27 -1 ${DATADIR}/ | ||
echo | echo | ||
- | echo " | + | echo " |
echo | echo | ||
echo " | echo " | ||
Line 45: | Line 47: | ||
< | < | ||
- | $ wget http://cab.spbu.ru/files/release3.11.1/SPAdes-3.11.1.tar.gz | + | $ wget https://github.com/ |
- | $ tar xf SPAdes-3.11.1.tar.gz | + | $ tar xf SPAdes-4.2.0-Linux.tar.gz |
- | $ cd SPAdes-3.11.1 | + | $ sudo cp -r SPAdes-4.2.0-Linux / |
- | $ sudo mkdir / | + | |
- | $ sudo chown aorth / | + | |
- | $ PREFIX=/ | + | |
- | $ sudo chown -R root: | + | |
Note: if you get the error '' | Note: if you get the error '' |
spades-software.1514234760.txt.gz · Last modified: by aorth