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spades-software [2015/06/09 19:38]
aorth
spades-software [2019/02/15 02:57] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.5.0+  * Version: 3.13.0
   * Added: September, 2014   * Added: September, 2014
-  * Updated: February, ​2015 +  * Updated: February, ​2019 
-  * Link: http://bioinf.spbau.ru/spades+  * Link: https://github.com/ablab/spades
  
 ===== Usage ===== ===== Usage =====
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 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 === === Example batch job ===
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 <​code>#​!/​bin/​env bash <​code>#​!/​bin/​env bash
 #SBATCH -p highmem #SBATCH -p highmem
-#SBATCH -n 6+#SBATCH -n 8
 #SBATCH -J spades #SBATCH -J spades
  
-module load spades/3.5.0+module load spades/3.6.1
  
 readonly DATADIR=~/​data/​bfusca readonly DATADIR=~/​data/​bfusca
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 mkdir -p ${OUTDIR} mkdir -p ${OUTDIR}
  
-# run spades with CPUs on mammoth (because 10/16 are already allocated)+# run spades with 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) # 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 -m 384+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 -m 384
  
 echo echo
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 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/release3.5.0/​SPAdes-3.5.0.tar.gz +$ tar xf SPAdes-3.13.0.tar.gz 
-$ tar xf SPAdes-3.5.0.tar.gz +$ cd SPAdes-3.13.0 
-$ cd SPAdes-3.5.0 +$ sudo mkdir /​export/​apps/​spades/​3.13.0 
-$ scl enable devtoolset-2 bash +$ sudo chown aorth /​export/​apps/​spades/​3.13.0 
-$ sudo mkdir -p /​export/​apps/​spades/​3.5.0 +$ sudo yum install centos-release-scl cmake 
-$ sudo chown aorth:aorth /​export/​apps/​spades/​3.5.0 +$ sudo yum install devtoolset-6-gcc.x86_64 devtoolset-6-gcc-c++.x86_64 
-$ PREFIX=/​export/​apps/​spades/​3.5.0 ./​spades_compile.sh +$ PREFIX=/​export/​apps/​spades/​3.13.0 ./​spades_compile.sh 
-$ sudo chown -R root:root /​export/​apps/​spades/​3.5.0</​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.1433867916.txt.gz · Last modified: 2015/06/09 19:38 by aorth