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spades-software [2019/10/04 12:58] – aorthspades-software [2022/02/21 17:48] – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.13.0+  * Version: 3.15 (3.15.4)
   * Added: September, 2014   * Added: September, 2014
-  * Updated: February, 2019+  * Updated: February, 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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 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/v3.15.4/SPAdes-3.15.4.tar.gz 
-$ tar xf SPAdes-3.13.0.tar.gz +$ tar xf SPAdes-3.15.4.tar.gz  
-$ cd SPAdes-3.13.0 +$ cd SPAdes-3.15.4 
-$ sudo mkdir /export/apps/spades/3.13.0 +$ sudo chown aorth /export/apps/spades/3.15 
-$ sudo chown aorth /export/apps/spades/3.13.0 +$ sudo mkdir -p /export/apps/spades/3.15 
-$ sudo yum install centos-release-scl cmake +$ scl enable devtoolset-7 bash 
-$ sudo yum install devtoolset-6-gcc.x86_64 devtoolset-6-gcc-c++.x86_64 +$ module load python/3.9 
-$ PREFIX=/export/apps/spades/3.13.0 ./spades_compile.sh +$ sed -i 's/^cmake/cmake3/' spades_compile.sh 
-$ sudo chown -R root:root /export/apps/spades/3.13.0</code>+$ PREFIX=/export/apps/spades/3.15 ./spades_compile.sh -j 4 
 +$ sudo chown -R root:root /export/apps/spades/3.15</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