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spades-software [2019/02/14 23:57] – aorthspades-software [2022/09/20 07:38] (current) – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.13.0+  * Version: 3.15 (3.15.5)
   * Added: September, 2014   * Added: September, 2014
-  * Updated: February, 2019+  * Updated: September, 2022
   * Link: https://github.com/ablab/spades   * Link: https://github.com/ablab/spades
  
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 Load one version into your environment and run it: Load one version into your environment and run it:
-<code>$ module load spades/3.13.0 +<code>$ module load spades/3.15 
-$ spades.py --help</code>+$ 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/3.6.1+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 "  ${OUTDIR}"</code>
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://github.com/ablab/spades/releases/download/v3.13.0/SPAdes-3.13.0.tar.gz +$ wget https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Linux.tar.gz 
-$ tar xf SPAdes-3.13.0.tar.gz +$ tar xf SPAdes-3.15.5-Linux.tar.gz 
-$ cd SPAdes-3.13.0 +$ sudo mv /export/apps/spades/3.15 /export/apps/spades/3.15.bak 
-$ sudo mkdir /export/apps/spades/3.13.0 +$ sed -i '1s/python/python3/' SPAdes-3.15.5-Linux/bin/spades.py 
-$ sudo chown aorth /export/apps/spades/3.13.0 +$ sudo cp -r SPAdes-3.15.5-Linux /export/apps/spades/3.15</code>
-$ sudo yum install centos-release-scl cmake +
-$ sudo yum install devtoolset-6-gcc.x86_64 devtoolset-6-gcc-c++.x86_64 +
-$ PREFIX=/export/apps/spades/3.13.0 ./spades_compile.sh +
-$ sudo chown -R root:root /export/apps/spades/3.13.0</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! 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.1550188667.txt.gz · Last modified: 2019/02/14 23:57 by aorth