Differences

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--- quast-software [2015/08/04 20:59] – [quast] aorth
+++ quast-software [2020/04/07 08:27] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== quast ======
 QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics.
 ===== Information =====
-  * Latest Version: 3.0
+  * Latest Version: 5.0.2
   * Added: September, 2014
-  * Updated: July, 2015
+  * Updated: April, 2020
-  * Link: http://bioinf.spbau.ru/en/quast
+  * Link: http://quast.sourceforge.net/quast
 ===== Usage =====
@@ 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/5.0.2
+$ 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-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</code>
+$ ./setup.py test
+$ 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>