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quast-software [2015/07/27 08:25]
joguya
quast-software [2020/04/07 08:27] (current)
aorth
Line 1: Line 1:
 ====== quast ====== ====== quast ======
 +QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics.
  
 ===== Information ===== ===== Information =====
  
-  * Latest Version: 3.0+  * Latest Version: 5.0.2
   * Added: September, 2014   * Added: September, 2014
-  * Updated: July2015 +  * Updated: April2020 
-  * Link: http://bioinf.spbau.ru/en/quast+  * Link: http://quast.sourceforge.net/quast
  
 ===== Usage ===== ===== Usage =====
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 See versions of quast which are available: See versions of quast which are available:
 <code>$ module avail quast</code> <code>$ module avail quast</code>
 +
 +Load one version into your environment and run it:
 +<code>$ module load quast/5.0.2
 +$ quast.py --help</code>
  
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>wget "http://downloads.sourceforge.net/project/quast/quast-3.0.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fquast%2Ffiles%2F&ts=1437982260&use_mirror=liquidtelecom" -O quast-3.0.tar.gz +<code>$ cd /tmp 
-tar -xvf quast-3.0.tar.gz +wget https://downloads.sourceforge.net/project/quast/quast-5.0.2.tar.gz 
-sudo mkdir -p /export/apps/quast/3.0 +$ tar xf quast-5.0.2.tar.gz 
-sudo cp -rv quast-3.0//export/apps/quast/3.0 +$ cd quast-5.0.2 
-sudo chown -R joguya:joguya /export/apps/quast/3.0 +sudo mkdir -p /export/apps/quast/5.0.2 
-cd /export/apps/quast/3.0 +sudo chown aorth /export/apps/quast/5.0.2 
-module load python/2.7.8 +$ python3 -m venv /export/apps/quast/5.0.2 
-cd libs/MUMmer3.23-linux +$ source /export/apps/quast/5.0.2/bin/activate 
-make +$ pip install --upgrade pip setuptools 
-cd - +$ pip install matplotlib 
-./metaquast.py --test +$ ./setup.py install_full 
-sudo chown -R root:root /export/apps/quast/3.0 +./setup.py test 
-</code>+sudo chown -R root:root /export/apps/quast/5.0.2</code>
  
-===== Running ===== +You can test the installation using the test data from the source tarball:
-After loading the module, consult the built-in help:+
  
-<code>metaquast.py --help</code>+<code>quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff</code>
quast-software.1437985532.txt.gz · Last modified: 2015/07/27 08:25 by joguya