Differences

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--- busco-software [2015/09/13 08:18] – [Information] aorth
+++ busco-software [2023/03/21 12:37] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== BUSCO ======
 BUSCO (Benchmarking Universal Single-Copy Orthologs) assesses genome assembly and annotation completeness with single-copy ortholog.
 ===== Information =====
-  * Latest Version: v1.1b
+  * Latest Version: 5.2.2
   * Added: August, 2015
-  * Link: http://busco.ezlab.org/#software
+  * Updated: December, 2021
+  * Link: https://busco.ezlab.org
 ===== Usage =====
@@ Line 14: / Line 14: @@
 <code>$ module avail BUSCO</code>
-===== Installation ======
+Load one version into your environment and run it:
-Notes from the sysadmin during installation:
+<code>$ module load BUSCO/5.2.2</code>
-<code>http://busco.ezlab.org/files/BUSCO_v1.1b1.tar.gz
-tar -xvf BUSCO_v1.1b1.tar.gz
-cd BUSCO_v1.1b1
-ln -s BUSCO_v1.1b1.py BUSCO_v1.1b.py
-chmod +x BUSCO_v1.1b1.py
-sudo mkdir -p /export/apps/BUSCO/v1.1b/
-sudo cp -r . /export/apps/BUSCO/v1.1b/</code>
-===== Running =====
 After loading the module, consult the built-in help:
-<code>$ BUSCO_v1.1b.py --help</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:
+<code>$ cp -r /export/apps/augustus/3.2.3/config /var/scratch/aorth-augustus-config
+$ export AUGUSTUS_CONFIG_PATH=/var/scratch/aorth-augustus-config</code>
+===== Installation ======
+Notes from the sysadmin during installation:
+<code>$ cd /tmp
+$ wget https://gitlab.com/ezlab/busco/-/archive/5.2.2/busco-5.2.2.tar.gz
+$ tar xf busco-5.2.2.tar.gz
+$ cd busco-5.2.2
+$ sudo mkdir /export/apps/BUSCO/5.2.2
+$ sudo chown aorth /export/apps/BUSCO/5.2.2
+$ python3 -m venv /export/apps/BUSCO/5.2.2
+$ source /export/apps/BUSCO/5.2.2/bin/activate
+$ pip install --upgrade setuptools pip
+$ pip install pandas biopython
+$ python setup.py install
+$ sudo cp scripts/generate_plot.py /export/apps/BUSCO/5.2.2/bin
+$ module load R/4.0
+$ mkdir /export/apps/BUSCO/5.2.2/r-libs
+$ 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>