Differences

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

--- pasta-software [2018/10/21 12:51] – created aorth
+++ pasta-software [2018/10/21 13:01] (current) – aorth
@@ Line 15: / Line 15: @@
 Load one version into your environment and run it:
 <code>$ module load pasta/git-d939adb2
-$ run_pasta.py -h</code>
+$ run_pasta.py -i input_fasta [-t starting_tree]</code>
 Consult the [[https://github.com/smirarab/pasta/blob/master/pasta-doc/pasta-tutorial.md|Pasta tutorial]] for more information.
@@ Line 22: / Line 22: @@
 Notes from the sysadmin during installation:
-<code></code>
+<code>$ cd /tmp
+$ mkdir pasta-code
+$ cd pasta-code
+$ git clone https://github.com/smirarab/pasta.git
+$ git clone https://github.com/smirarab/sate-tools-linux.git
+$ git clone https://github.com/kodicollins/pasta-databases sate-tools-linux/pasta-databases
+$ cd pasta
+$ sudo mkdir -p /export/apps/pasta/git-d939adb2/lib/python2.7/site-packages
+$ sudo chown -R aorth /export/apps/pasta/git-d939adb2
+$ export PYTHONPATH=/export/apps/pasta/git-d939adb2/lib/python2.7/site-packages
+$ python setup.py develop --prefix=/export/apps/pasta/git-d939adb2
+$ cd ..
+$ sudo cp -r sate-tools-linux/ /export/apps/pasta/git-d939adb2
+$ sudo chown -R root:root /export/apps/pasta/git-d939adb2
+# for graphical interface (use on HPC only to avoid installing stupid dependencies on nodes)
+$ sudo yum install wxPython.x86_64</code>
 Note that the Pasta project does not tag their releases, so I've used the git commit hash at the time of installation.