Differences

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--- busco-software [2017/09/11 13:07] – aorth
+++ busco-software [2023/03/21 12:37] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest Version: 3.0.2
+  * Latest Version: 5.2.2
   * Added: August, 2015
-  * Updated: September, 2017
+  * Updated: December, 2021
-  * Link: http://busco.ezlab.org
+  * Link: https://busco.ezlab.org
 ===== Usage =====
@@ Line 14: / Line 14: @@
 <code>$ module avail BUSCO</code>
-Load one version into your environment:
+Load one version into your environment and run it:
-<code>$ module load BUSCO/3.0.2</code>
+<code>$ module load BUSCO/5.2.2</code>
 After loading the module, consult the built-in help:
-<code>$ run_BUSCO.py -h</code>
+<code>$ busco -h</code>
+See the BUSCO documentation for more information about how to use it: https://busco.ezlab.org/busco_userguide.html#running-busco
 Note: BUSCO utilizes Augustus and requires you to make a copy of the Augustus configuration for each of your runs as well as set up an environment variable pointing to it, ie:
@@ Line 30: / Line 32: @@
 <code>$ cd /tmp
-$ git clone https://gitlab.com/ezlab/busco.git
+$ wget https://gitlab.com/ezlab/busco/-/archive/5.2.2/busco-5.2.2.tar.gz
-$ cd busco
+$ tar xf busco-5.2.2.tar.gz
-$ git checkout 3.0.2
+$ cd busco-5.2.2
-$ module load python/3.6.1
+$ sudo mkdir /export/apps/BUSCO/5.2.2
-$ sudo mkdir /export/apps/BUSCO/3.0.2
+$ sudo chown aorth /export/apps/BUSCO/5.2.2
-$ sudo chown aorth /export/apps/BUSCO/3.0.2
+$ python3 -m venv /export/apps/BUSCO/5.2.2
-$ python -m venv /export/apps/BUSCO/3.0.2
+$ source /export/apps/BUSCO/5.2.2/bin/activate
-$ . /export/apps/BUSCO/3.0.2/bin/activate
+$ pip install --upgrade setuptools pip
+$ pip install pandas biopython
 $ python setup.py install
-$ cp -rv * /export/apps/BUSCO/3.0.2
+$ sudo cp scripts/generate_plot.py /export/apps/BUSCO/5.2.2/bin
-$ cp /export/apps/BUSCO/3.0.2/config/config.ini.default /export/apps/BUSCO/3.0.2/config/config.ini
+$ module load R/4.0
-# edit paths in /export/apps/BUSCO/3.0.2/config/config.ini
+$ mkdir /export/apps/BUSCO/5.2.2/r-libs
-$ sudo chown -R root:root /export/apps/BUSCO/3.0.2</code>
+$ R_LIBS=/export/apps/BUSCO/5.2.2/r-libs Rscript -e 'install.packages("ggplot2", repos="https://cran.rstudio.com")'
+$ sudo chown -R root:root /export/apps/BUSCO/5.2.2</code>
-Consult the file ''BUSCO_v3_userguide.pdf'' for more installation and usage tips.