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--- cluster:73 [2022/10/18 09:21]
hmeij07 [Sequencing Tools #3]
+++ cluster:73 [2022/12/01 13:57]
hmeij07 [HPC SDK]
@@ Line 23: / Line 23: @@
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== Trimmomatic ======
+  * http://www.usadellab.org/cms/?page=trimmomatic
+  * binary download and stage
+<code>
+/share/apps/CENTOS6/Trimmomatic-0.39/
+[root@cottontail Trimmomatic-0.39]# ll
+total 176
+drwxr-xr-x 2 root root      8 Apr  8  2019 adapters
+-rw-r--r-- 1 root root  35147 May 16  2018 LICENSE
+-rw-r--r-- 1 root root 128502 Apr  8  2019 trimmomatic-0.39.jar
+</code>
@@ Line 327: / Line 345: @@
 ** Flye **
-Somewhat annoying, no miniconda3 package, so local install, use minconda3 environment as listed top of this section (python 3.9, gcc 9.2
+Somewhat annoying, no miniconda3 package, so local install, use minconda3 environment as listed top of this section (python 3.9, gcc 9.2)
-  * v2.9.1 (october 2022)
+  * v2.9.1 (October 2022)
   * python bin/flye
-    * chnage the PATHs accordingly
+    * change the PATHs accordingly
 <code>
@@ Line 340: / Line 358: @@
 </code>
-  * v2.9 (august 2021)
+  * v2.9 (August 2021)
   * python bin/flye
@@ Line 688: / Line 706: @@
 IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020
+</code>
+  * https://userguide.mdanalysis.org/stable/installation.html
+  * calterlab, annika (used pip to install)
+<code>
+Successfully installed
+GridDataFormats-1.0.1 MDAnalysis-2.3.0
+fasteners-0.18 mmtf-python-1.1.3
+mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4
 </code>

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