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--- cluster:73 [2023/07/04 12:22]
hmeij07 [Sequencing Tools #3]
+++ cluster:73 [2023/07/12 14:15]
hmeij07 [Trimmomatic]
@@ Line 26: / Line 26: @@
-====== Trimmomatic ======
+===== Masurca =====
+    module: masurca/4.1.0
+    https://github.com/alekseyzimin/masurca/releases
+    supports openmp (maybe)
+    queues mwgpu, exx96 (centos 7)
+<code>
+export PATH=/share/apps/CENTOS7/masurca/4.1.0/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/masurca/4.1.0/lib:$LD_LIBRARY_PATH
+</code>
+===== Trimmomatic =====
   * http://www.usadellab.org/cms/?page=trimmomatic
@@ Line 346: / Line 362: @@
 ** Flye **
-Somewhat annoying, no miniconda3 package, so local install, use minconda3 environment as listed top of this section (python 3.9, gcc 9.2). Local building (without installation) on centos7 greentail52.
+Somewhat annoying, no miniconda3 package, (python 3.9, gcc 9.2). Local building (without installation) on centos7 greentail52.
+  * setup env as for all packages in #3, see top of section
   * v2.9.2 (June 2023)
   * python bin/flye
-    * chnage the PATHS accordingly
+    * change the PATHS accordingly
 <code>
@@ Line 1091: / Line 1108: @@
 pcangsd --version
 pcangsd 1.10
+</code>
+  * **angsd**, requires miniconda3, same environment as pcangsd
+  * http://www.popgen.dk/angsd/index.php/RealSFS
+  * add location of angsd to PATH env
+<code>
+$ pwd
+/share/apps/CENTOS7/angsd/0.940/angsd
+$ ls -l angsd
+-rwxr-xr-x 1 hmeij its 5517248 Jul  6 14:11 angsd
+$ ./angsd
+	-> angsd version: 0.940-dirty (htslib: 1.16) build(Jul  6 2023 14:11:30)
 </code>

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