Differences

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--- medaka-software [2019/09/03 22:12] – created aorth
+++ medaka-software [2025/05/13 12:27] (current) – aorth
@@ Line 2: / Line 2: @@
 medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.
-  * Latest Version: 0.8.2
+  * Latest Version: 1.12.1
   * Added: September, 2019
+  * Updated: May, 2025
   * Link: https://github.com/nanoporetech/medaka
 ===== Usage =====
-Show all available versions of medaka:
+Show which versions are available:
 <code>$ module avail medaka</code>
-Load a particular version of medaka into your environment and run it:
+Load one version into your environment and run it:
-<code>$ module load medaka/0.8.2
+<code>$ module load medaka/1.12.1
-$ medaka</code>
+$ medaka -h</code>
 ===== Installation =====
 Notes from the sysadmin during installation:
-<code>$ sudo mkdir -p /export/apps/medaka/v0.8.2
+<code>$ module load python/3.10
-$ sudo chown aorth /export/apps/medaka/v0.8.2
+$ sudo mkdir -p /export/apps/medaka/1.12.1/.venv
-$ python3 -m venv /export/apps/medaka/v0.8.2
+$ sudo chown aorth /export/apps/medaka/1.12.1/.venv
-$ source /export/apps/medaka/v0.8.2/bin/activate
+$ python -m venv /export/apps/medaka/1.12.1/.venv
-$ pip install --upgrade pip setuptools
+$ source /export/apps/medaka/1.12.1/.venv/bin/activate
-$ pip install medaka
+$ python -m pip install -U pip setuptools wheel
-$ sudo chown -R root:root </code>
+$ python -m pip install medaka==1.12.1
+$ sudo chown -R root:root /export/apps/medaka/1.12.1</code>
-This uses the CentOS 7 system's Python 3.6 environment.