Differences

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

--- srst2-software [2023/08/10 07:31] – created aorth
+++ srst2-software [2023/08/10 07:43] (current) – aorth
@@ Line 7: / Line 7: @@
   * Version: git-73f885f5
   * Added: August, 2023
-  * Link: https://github.com/katholt/srst2/
+  * Link: https://github.com/katholt/srst2
 ===== Usage =====
@@ Line 17: / Line 17: @@
 <code>$ module load srst2/git-73f885f5
 $ srst2 --version</code>
+**Note:** Please use the %%''--threads''%% option to tell panaroo how many CPU cores/threads it should use. This number should match the number of CPUs you requested in your SLURM batch allocation.
 ===== Installation ======
@@ Line 22: / Line 24: @@
 Notes from the sysadmin during installation:
-<code></code>
+<code>$ module load python/2.7
+$ sudo mkdir -p /export/apps/srst2/git-73f885f5
+$ sudo chown aorth:aorth /export/apps/srst2/git-73f885f5
+$ virtualenv /export/apps/srst2/git-73f885f5/venv
+$ source /export/apps/srst2/git-73f885f5/venv/bin/activate
+$ pip install scipy
+$ pip install git+https://github.com/katholt/srst2
+$ sudo chown -R root:root /export/apps/srst2/git-73f885f5</code>
 See also, the [[https://github.com/bioconda/bioconda-recipes/blob/master/recipes/srst2/meta.yaml|bioconda recipe for srst2]].