Differences

This shows you the differences between two versions of the page.

--- busco-software [2020/05/12 15:45] – aorth
+++ busco-software [2023/03/21 12:37] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest Version: 4.0.6
+  * Latest Version: 5.2.2
   * Added: August, 2015
-  * Updated: May, 2020
+  * Updated: December, 2021
   * Link: https://busco.ezlab.org
@@ Line 15: / Line 15: @@
 Load one version into your environment and run it:
-<code>$ module load BUSCO/4.0.6</code>
+<code>$ module load BUSCO/5.2.2</code>
 After loading the module, consult the built-in help:
 <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 4.0.6
+$ cd busco-5.2.2
-$ sudo mkdir /export/apps/BUSCO/4.0.6
+$ sudo mkdir /export/apps/BUSCO/5.2.2
-$ sudo chown aorth /export/apps/BUSCO/4.0.6
+$ sudo chown aorth /export/apps/BUSCO/5.2.2
-$ python3 -m venv /export/apps/BUSCO/4.0.6
+$ python3 -m venv /export/apps/BUSCO/5.2.2
-$ source /export/apps/BUSCO/4.0.6/bin/activate
+$ source /export/apps/BUSCO/5.2.2/bin/activate
 $ pip install --upgrade setuptools pip
+$ pip install pandas biopython
 $ python setup.py install
-$ module load R/3.6
+$ sudo cp scripts/generate_plot.py /export/apps/BUSCO/5.2.2/bin
-$ mkdir /export/apps/BUSCO/4.0.6/r-libs
+$ module load R/4.0
-$ export R_LIBS=/export/apps/BUSCO/4.0.6/r-libs
+$ mkdir /export/apps/BUSCO/5.2.2/r-libs
-$ Rscript -e 'install.packages("ggplot2", repos="https://cran.rstudio.com")'
+$ R_LIBS=/export/apps/BUSCO/5.2.2/r-libs Rscript -e 'install.packages("ggplot2", repos="https://cran.rstudio.com")'
-$ module load blast/2.2.31+ augustus/3.2.3 hmmer/3.2.1 sepp/4.3.8 prodigal/2.6.3
+$ sudo chown -R root:root /export/apps/BUSCO/5.2.2</code>
-$ ./scripts/busco_configurator.py config/config.ini config/myconfig.ini
-$ sudo cp config/myconfig.ini  /export/apps/BUSCO/4.0.6/
-$ sudo chown -R root:root /export/apps/BUSCO/4.0.6</code>
-Consult the [[https://busco.ezlab.org/busco_userguide.html|BUSCO user guide]] for more installation and usage tips.