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spades-software [2014/09/22 19:08]
aorth
spades-software [2019/02/15 02:57] (current)
aorth
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-====== ​spades ​======+====== ​SPAdes ​====== 
 +SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
  
 ===== Information ===== ===== Information =====
  
-  * Version: 3.1.1+  * Version: 3.13.0
   * Added: September, 2014   * Added: September, 2014
-  * Link: http://bioinf.spbau.ru/spades+  ​* Updated: February, 2019 
 +  ​* Link: https://github.com/ablab/spades
  
 ===== Usage ===== ===== Usage =====
  
-=== 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/​3.13.0 
 +$ spades.py --help</​code>​ 
 + 
 +=== Example batch job === 
 + 
 +<​code>​#!/bin/env bash 
 +#SBATCH -p highmem 
 +#SBATCH -n 8 
 +#SBATCH -J spades 
 + 
 +module ​load spades/3.6.1 
 + 
 +readonly DATADIR=~/​data/​bfusca 
 +readonly OUTDIR=/​var/​scratch/​aorth-spades-oct8 
 + 
 +# create output directory 
 +mkdir -p ${OUTDIR} 
 + 
 +# run spades with 8 CPUs on mammoth (it has 16 logical CPUs, but only 8 are physical) 
 +# run spades with 384 GB of RAM (default is 250, but it ran out of memory before) 
 +spades.py -k 27 -1 ${DATADIR}/​1_S1_L001_R1_001_val_1.fastq.gz -2 ${DATADIR}/​1_S1_L001_R2_001_val_2.fastq.gz -o ${OUTDIR} -t 8 -m 384 
 + 
 +echo 
 +echo "​Remember to check (and clean!) output directory on mammoth:"​ 
 +echo 
 +echo " ​ ${OUTDIR}"​</​code>​
  
 ===== Installation ====== ===== Installation ======
 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/​v3.13.0/SPAdes-3.13.0.tar.gz 
-wget http://spades.bioinf.spbau.ru/release3.1.1/SPAdes-3.1.1.tar.gz +$ tar xf SPAdes-3.13.0.tar.gz 
-cd SPAdes-3.1.+$ cd SPAdes-3.13.0 
-sed -i '​s/​cmake/​cmake28/'​ spades_compile.sh +sudo mkdir /​export/​apps/​spades/​3.13.0 
-scl enable devtoolset-1.1 bash +sudo chown aorth /​export/​apps/​spades/​3.13.0 
-sudo mkdir -p /​export/​apps/​spades/​3.1.1 +$ sudo yum install centos-release-scl cmake 
-sudo chown aorth:aorth /​export/​apps/​spades/​3.1.1 +$ sudo yum install devtoolset-6-gcc.x86_64 devtoolset-6-gcc-c++.x86_64 
-PREFIX=/​export/​apps/​spades/​3.1../​spades_compile.sh +PREFIX=/​export/​apps/​spades/​3.13../​spades_compile.sh 
-sudo chown -R root:root /​export/​apps/​spades/​3.1.1</​code>​ +sudo chown -R root:root /​export/​apps/​spades/​3.13.0</​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.1411402098.txt.gz · Last modified: 2014/09/22 19:08 by aorth