Differences

This shows you the differences between two versions of the page.

--- spades-software [2017/07/06 14:15] – aorth
+++ spades-software [2022/02/21 17:48] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 3.10.1
+  * Version: 3.15 (3.15.4)
   * Added: September, 2014
-  * Updated: July, 2017
+  * Updated: February, 2022
-  * Link: http://cab.spbu.ru/software/spades/
+  * Link: https://github.com/ablab/spades
 ===== Usage =====
@@ Line 13: / Line 13: @@
 See versions of spades which are available:
 <code>$ module avail spades</code>
+Load one version into your environment and run it:
+<code>$ module load spades/3.15
+$ spades.py --help
+$ spades.py --test</code>
 === Example batch job ===
@@ Line 21: / Line 26: @@
 #SBATCH -J spades
-module load spades/3.6.1
+module load spades/3.13.0
 readonly DATADIR=~/data/bfusca
@@ Line 34: / Line 39: @@
 echo
-echo "Remember to check (and clean!) output directory on mammoth:"
+echo "Remember to check (and clean!) output directory on compute07:"
 echo
 echo "  ${OUTDIR}"</code>
@@ Line 42: / Line 47: @@
 <code>$ 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/v3.15.4/SPAdes-3.15.4.tar.gz
-$ tar xf SPAdes-3.10.1-Linux.tar.gz
+$ tar xf SPAdes-3.15.4.tar.gz
-$ sudo mkdir /export/apps/spades/3.10.1
+$ cd SPAdes-3.15.4
-$ sudo cp -rv SPAdes-3.10.1-Linux/* /export/apps/spades/3.10.1</code>
+$ sudo chown aorth /export/apps/spades/3.15
+$ sudo mkdir -p /export/apps/spades/3.15
-===== Running =====
+$ scl enable devtoolset-7 bash
-After loading the module, consult the built-in help:
+$ module load python/3.9
+$ sed -i 's/^cmake/cmake3/' spades_compile.sh
+$ PREFIX=/export/apps/spades/3.15 ./spades_compile.sh -j 4
+$ sudo chown -R root:root /export/apps/spades/3.15</code>
-<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!