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spades-software [2017/07/06 17:37]
aorth
spades-software [2019/10/04 15:58] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.10.1+  * Version: 3.13.0
   * Added: September, 2014   * Added: September, 2014
-  * Updated: ​July2017 +  * Updated: ​February2019 
-  * 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/release3.10.1/SPAdes-3.10.1-Linux.tar.gz +$ wget https://github.com/​ablab/​spades/​releases/download/v3.13.0/SPAdes-3.13.0.tar.gz 
-$ tar xf SPAdes-3.10.1-Linux.tar.gz +$ tar xf SPAdes-3.13.0.tar.gz 
-$ sudo mkdir /​export/​apps/​spades/​3.10.1 +$ cd SPAdes-3.13.0 
-$ sudo cp -rv SPAdes-3.10.1-Linux//​export/​apps/​spades/​3.10.1</​code>​+$ sudo mkdir /​export/​apps/​spades/​3.13.0 
 +$ sudo chown aorth /​export/​apps/​spades/​3.13.0 
 +$ 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!
spades-software.1499351852.txt.gz · Last modified: 2017/07/06 17:37 by aorth