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--- quast-software [2017/10/04 05:03] – aorth
+++ quast-software [2017/10/04 07:09] – aorth
@@ Line 1: / Line 1: @@
 ====== quast ======
 QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics.
 ===== Information =====
   * Latest Version: 3.0
   * Added: September, 2014
-  * Updated: July, 2015
+  * Updated: September, 2017
   * Link: http://quast.sourceforge.net/quast
@@ Line 12: / Line 13: @@
 See versions of quast which are available:
 <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 ======
 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/3.0
+$ 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>