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spades-software [2016/08/15 13:30] – [Information] joguyaspades-software [2022/02/21 17:48] – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.6.0+  * Version: 3.15 (3.15.4)
   * Added: September, 2014   * Added: September, 2014
-  * Updated: August, 2016 +  * Updated: February, 2022 
-  * 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:
 <code>$ module avail spades</code> <code>$ module avail spades</code>
 +
 +Load one version into your environment and run it:
 +<code>$ module load spades/3.15
 +$ spades.py --help
 +$ spades.py --test</code>
  
 === 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=~/data/bfusca readonly DATADIR=~/data/bfusca
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 echo echo
-echo "Remember to check (and clean!) output directory on mammoth:"+echo "Remember to check (and clean!) output directory on compute07:"
 echo echo
 echo "  ${OUTDIR}"</code> echo "  ${OUTDIR}"</code>
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 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>$ sudo yum install cmake28.x86_64 +<code>$ cd /tmp 
-$ cd /tmp +$ wget https://github.com/ablab/spades/releases/download/v3.15.4/SPAdes-3.15.4.tar.gz 
-$ wget http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz +$ tar xf SPAdes-3.15.4.tar.gz  
-$ tar xf SPAdes-3.5.0.tar.gz +$ cd SPAdes-3.15.4 
-$ cd SPAdes-3.5.0 +$ sudo chown aorth /export/apps/spades/3.15 
-$ scl enable devtoolset-2 bash +$ sudo mkdir -p /export/apps/spades/3.15 
-$ sudo mkdir -p /export/apps/spades/3.5.0 +$ scl enable devtoolset-7 bash 
-$ sudo chown aorth:aorth /export/apps/spades/3.5.0 +$ module load python/3.9 
-$ PREFIX=/export/apps/spades/3.5.0 ./spades_compile.sh +$ sed -i 's/^cmake/cmake3/' spades_compile.sh 
-$ sudo chown -R root:root /export/apps/spades/3.5.0</code> +$ PREFIX=/export/apps/spades/3.15 ./spades_compile.sh -j 4 
- +$ sudo chown -R root:root /export/apps/spades/3.15</code>
-===== Running ===== +
-After loading the module, consult the built-in help:+
  
-<code>$ spades.py --help</code>+Note: if you get the error ''Exception caught basic_string::_S_construct null not valid'' you need to call the spades.py script, not the spades binary!
spades-software.txt · Last modified: 2022/09/20 07:38 by aorth