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--- cluster:73 [2022/04/07 14:50]
hmeij07
+++ cluster:73 [2022/04/25 18:52]
hmeij07 [Paleogenomics Tools]
@@ Line 318: / Line 318: @@
 ** Flye **
+Somewhat annoying, no miniconda3 package, so local install, use minconda3 env
+  * v2.9
+  * python bin/flye
+<code>
+export PATH=/share/apps/CENTOS7/flye/2.9/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/flye/2.9/lib:$LD_LIBRARY_PATH
+which flye
+/share/apps/CENTOS7/flye/2.9/bin/flye
+flye --version
+.9-b1774
+</code>
   * https://github.com/fenderglass/Flye
@@ Line 945: / Line 961: @@
 [hmeij@petaltail ~]$ mapDamage --version
 .0.6
+</code>
+  * **PCAngsd**, requires miniconda3's python
+  * https://github.com/Rosemeis/pcangsd
+<code>
+source /share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh
+export PATH=/share/apps/CENTOS7/amber/miniconda3/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/lib:$LD_LIBRARY_PATH
+which pcangsd
+/share/apps/CENTOS7/amber/miniconda3/bin/pcangsd
+pcangsd --version
+pcangsd 1.10
+</code>
+  * **Standard RAxML version**
+  * https://github.com/stamatak/standard-RAxML
+<code>
+# add path to $PATH
+[hmeij@greentail52 tmp]$ ll /share/apps/CENTOS7/raxml/8.2.12/
+total 3202
+-rwxr-xr-x 1 hmeij its 1177632 Apr 25 14:49 raxmlHPC-AVX
+-rwxr-xr-x 1 hmeij its 1177632 Apr 25 14:49 raxmlHPC-AVX2
+-rwxr-xr-x 1 hmeij its 1152040 Apr 25 14:49 raxmlHPC_serial
+-rwxr-xr-x 1 hmeij its 1185704 Apr 25 14:49 raxmlHPC-SSE3
 </code>

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