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--- cluster:73 [2022/03/18 19:21]
hmeij07 [OpenHPC]
+++ cluster:73 [2022/04/25 13:47]
hmeij07 [Sequencing Tools #3]
@@ Line 3: / Line 3: @@
 ====== Software ======
+[[cluster:215|OpenHPC Software]] for **Rocky 8**
+Below is all centos 6 and/or 7, which may or may not run in 8.
 IMPORTANT NOTE: **Since moving to the TrueNAS/ZFS appliance all references to** ''/home/apps'' **should be replaced with** ''/share/apps'' **which points to** ''/zfshomes/apps''
@@ Line 313: / 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 919: / Line 940: @@
 </code>
+  * **mapDamage2**
+  * https://github.com/ginolhac/mapDamage/issues/25
+  * docker container is broke
+  * requires centos6 so queues hp12, mw128  .. may run elsewhere?
+  * conda install -c 'bioconda' mapdamage2
+<code>
+# env
+export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
+export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
+The following NEW packages will be INSTALLED:
+  mapdamage2         bioconda/linux-64::mapdamage2-2.0.6-1
+  pysam              bioconda/linux-64::pysam-0.16.0.1-py27hc729bab_3
+  seqtk              bioconda/linux-64::seqtk-1.3-h5bf99c6_3
+[hmeij@petaltail ~]$ mapDamage --version
+.0.6
+</code>

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