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quast-software [2017/10/04 05:03]
quast-software [2017/10/04 07:09]
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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:   * Link:
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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
 +$ --help</code>
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
-<code>$ wget "" -O quast-3.0.tar.gz +<code>$ cd /tmp 
-tar -xvf quast-3.0.tar.gz +$ wget 
-$ 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 
-$ ./ --test +$ ./ 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> --help</code>+<code> 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: 2020/04/07 08:27 by aorth