Differences

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--- cutadapt-software [2015/06/24 09:08] – aorth
+++ cutadapt-software [2021/12/15 07:33] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: v1.8.1
+  * Version: 3.5
   * Added: June, 2015
+  * Updated: December, 2021
   * Link: https://github.com/marcelm/cutadapt
 ===== Usage =====
-=== See versions of cutadapt which are available ===
+See available versions of cutadapt:
-<code>module avail cutadapt</code>
+<code>$ module avail cutadapt</code>
+Load one version into your environment and run it:
+<code>$ module load cutadapt/3.5
+$ cutadapt</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>$ sudo mkdir -p /export/apps/cutadapt/v1.8.1
+<code>$ sudo mkdir -p /export/apps/cutadapt/3.5
-$ module load python/2.7.8
+$ sudo chown aorth /export/apps/cutadapt/3.5
-$ sudo chown aorth /export/apps/cutadapt/v1.8.1
+$ python3 -m venv /export/apps/cutadapt/3.5
-$ pip install cutadapt --install-option="--prefix=/export/apps/cutadapt/v1.8.1"
+$ source /export/apps/cutadapt/3.5/bin/activate
-$ sudo chown root:root /export/apps/cutadapt/v1.8.1</code>
+$ pip install --upgrade setuptools pip
+$ pip install cutadapt==3.5
+$ sudo chown -R root:root /export/apps/cutadapt/3.5</code>
+Installation is greatly simplified by using Python 3's built-in venv module to create a dedicated environment, then use standard pip to install cutadapt and its dependencies.