Differences

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--- sepp-software [2020/05/12 08:13] – created aorth
+++ sepp-software [2021/12/28 13:49] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 4.3.8
+  * Version: 4.5.1
   * Added: May, 2020
+  * Updated: December, 2021
   * Link: https://github.com/smirarab/sepp
@@ Line 15: / Line 16: @@
 Load one version into your environment and run it:
-<code>$ module load sepp/4.3.8
+<code>$ module load sepp/4.5.1
-$ run_sepp.py</code>
+$ run_sepp.py -h</code>
+The general command for running SEPP is:
+<code>run_sepp.py -t <tree_file> -a <alignment_file> -f <fragment_file> -r <raxml_info_file> -A <alignment_set_size> -P <placement_set_size></code>
+**Note:** please use the "-x" or "--cpu" options to set the number of CPUs for your SEPP run. This number should match the number of CPUs requested in your SBATCH allocation.
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>$ sudo mkdir -p /export/apps/sepp/4.3.8
+<code>$ sudo mkdir -p /export/apps/sepp/4.5.1
-$ sudo chown aorth /export/apps/sepp/4.3.8
+$ sudo chown aorth:aorth /export/apps/sepp/4.5.1
-$ git clone https://github.com/smirarab/sepp.git -b 4.3.8 /export/apps/sepp/4.3.8
+$ git clone https://github.com/smirarab/sepp.git -b 4.5.1 /export/apps/sepp/4.5.1
-$ cd /export/apps/sepp/4.3.8
+$ cd /export/apps/sepp/4.5.1
 $ python3 -m venv venv
 $ source venv/bin/activate
+$ pip install --upgrade pip setuptools
 $ python setup.py config -c
 $ python setup.py install
-$ sed -i 's?/usr/bin/env python?/usr/bin/env python3?' run_sepp.py
+$ sed -i 's?/usr/bin/env python?/usr/bin/env python3?' run_*.py split_sequences.py
-$ sudo chown -R root:root /export/apps/sepp/4.3.8</code>
+$ sudo chown -R root:root /export/apps/sepp/4.5.1</code>
 Sepp's setup script wants to write the ''main.config'' file in the user's home directory or the source directory, so we need to clone the git repository to ''/export/apps'' where we intend to install it and then use the local (''-c'') config option.