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--- quast-software [2014/09/29 10:33] – created aorth
+++ quast-software [2017/10/04 05:03] – aorth
@@ Line 1: / Line 1: @@
 ====== quast ======
+QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics.
 ===== Information =====
-  * Version: 2.3
+  * Latest Version: 3.0
   * Added: September, 2014
-  * Link: http://bioinf.spbau.ru/en/quast
+  * Updated: July, 2015
+  * Link: http://quast.sourceforge.net/quast
 ===== Usage =====
-=== See versions of quast which are available ===
+See versions of quast which are available:
-<code>module avail quast</code>
+<code>$ module avail quast</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>cd /tmp
+<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
-wget 'http://downloads.sourceforge.net/project/quast/quast-2.3.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fquast%2Ffiles%2F&ts=1411971659&use_mirror=tenet' -O quast-2.3.tar.gz
+$ tar -xvf quast-3.0.tar.gz
-tar xf quast-2.3.tar.gz
+$ sudo mkdir -p /export/apps/quast/3.0
-sudo mkdir -p /export/apps/quast
+$ sudo cp -rv quast-3.0/* /export/apps/quast/3.0
-sudo cp -rv quast-2.3 /export/apps/quast/2.3
+$ sudo chown -R joguya:joguya /export/apps/quast/3.0
-sudo chown -R aorth:aorth /export/apps/quast/2.3
+$ cd /export/apps/quast/3.0
-cd /export/apps/quast/2.3
+$ module load python/2.7.8
-module load python/2.7.6
+$ cd libs/MUMmer3.23-linux
-./metaquast.py --test
+$ make
-cd libs/MUMmer3.23-linux
+$ cd -
-make
+$ ./metaquast.py --test
-cd ../..
+$ sudo chown -R root:root /export/apps/quast/3.0</code>
-./metaquast.py --test
-sudo chown -R root:root /export/apps/quast/2.3</code>
 ===== Running =====
 After loading the module, consult the built-in help:
-<code>metaquast.py  --help</code>
+<code>$ metaquast.py --help</code>