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quast-software [2017/10/04 08:03]
aorth
quast-software [2017/10/04 10:09] (current)
aorth
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 ====== quast ====== ====== quast ======
 QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics. QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics.
 +
 ===== Information ===== ===== Information =====
  
   * Latest Version: 3.0   * Latest Version: 3.0
   * Added: September, 2014   * Added: September, 2014
-  * Updated: ​July2015+  * Updated: ​September2017
   * Link: http://​quast.sourceforge.net/​quast   * Link: http://​quast.sourceforge.net/​quast
  
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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/4.5
 +$ 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-4.5.tar.gz 
-$ sudo mkdir -p /​export/​apps/​quast/​3.0 +$ tar xf quast-4.5.tar.gz 
-$ sudo cp -rv quast-3.0/​* ​/​export/​apps/​quast/​3.0 +cd quast-4.5 
-sudo chown -R joguya:​joguya ​/​export/​apps/​quast/​3.0 +$ sudo mkdir -p /​export/​apps/​quast/​4.5 
-cd /​export/​apps/​quast/​3.+$ sudo chown aorth /​export/​apps/​quast/4.5 
-$ module load python/2.7.8 +$ $ module load python/3.5.3 
-$ cd libs/MUMmer3.23-linux +python ​-m venv /​export/​apps/​quast/​4.5 
-make +/​export/​apps/​quast/​4.5/bin/activate 
-$ cd +pip install ​-U setuptools pip 
-$ ./metaquast.py --test +$ ./setup.py install_full 
-$ sudo chown -R root:root /​export/​apps/​quast/​3.0</​code>​+$ sudo chown -R root:root /​export/​apps/​quast/​4.5</​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.txt · Last modified: 2017/10/04 10:09 by aorth