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spades-software [2017/12/25 20:45] – aorthspades-software [2019/10/04 12:58] – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.10.1+  * Version: 3.13.0
   * Added: September, 2014   * Added: September, 2014
-  * Updated: July, 2017 +  * Updated: February, 2019 
-  * Link: http://cab.spbu.ru/software/spades/+  * Link: https://github.com/ablab/spades
  
 ===== Usage ===== ===== Usage =====
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 <code>$ module avail spades</code> <code>$ module avail spades</code>
  
-After loading the module, consult the built-in help: +Load one version into your environment and run it: 
-<code>$ spades.py --help</code>+<code>$ module load spades/3.13.0 
 +$ spades.py --help</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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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget  http://cab.spbu.ru/files/release3.11.1/SPAdes-3.11.1.tar.gz +$ wget https://github.com/ablab/spades/releases/download/v3.13.0/SPAdes-3.13.0.tar.gz 
-$ tar xf SPAdes-3.11.1.tar.gz +$ tar xf SPAdes-3.13.0.tar.gz 
-$ cd SPAdes-3.11.1 +$ cd SPAdes-3.13.0 
-$ sudo mkdir /export/apps/spades/3.11.1 +$ sudo mkdir /export/apps/spades/3.13.0 
-$ sudo chown aorth /export/apps/spades/3.11.1 +$ sudo chown aorth /export/apps/spades/3.13.0 
-$ PREFIX=/export/apps/spades/3.11.1 ./spades_compile.sh +$ sudo yum install centos-release-scl cmake 
-$ sudo chown -R root:root /export/apps/spades/3.11.1</code>+$ 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.txt · Last modified: 2022/09/20 07:38 by aorth