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--- cluster:73 [2022/03/02 10:00]
hmeij07 [Magenta]
+++ cluster:73 [2022/11/07 13:59]
hmeij07 [Miniconda3]
@@ 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 218: / Line 223: @@
 Suite of tools for high-accuracy basecaling, assembly, polishing, and alignment. Installed in a specific miniconda3 environment (see below).
-  * Requires centos7 so queues mwgpu, amber128, exx96
+  * Requires centos7 so queues mwgpu, <del>amber128</del>, exx96
     * debug server greentail52
   * PREFIX=/share/apps/CENTOS7/miniconda3
@@ Line 228: / Line 233: @@
 <code>
-# environment
+# environment for all modules
 source /share/apps/CENTOS7/miniconda3/etc/profile.d/conda.sh
 export PATH=/share/apps/CENTOS7/miniconda3/bin:$PATH
@@ Line 239: / Line 244: @@
 which conda python pip mpirun gcc cmake
 python --version
+/share/apps/CENTOS7/miniconda3/bin/conda
+/share/apps/CENTOS7/miniconda3/bin/python
+/share/apps/CENTOS7/miniconda3/bin/pip
+/share/apps/CENTOS7/miniconda3/bin/mpirun
+/share/apps/CENTOS7/gcc/9.2.0/bin/gcc
+/share/apps/CENTOS7/cmake/3.12.1/bin/cmake
 </code>
@@ Line 313: / Line 326: @@
 ** Flye **
+Somewhat annoying, no miniconda3 package, so local install, use minconda3 environment as listed top of this section (python 3.9, gcc 9.2)
+  * v2.9.1 (October 2022)
+  * python bin/flye
+    * change the PATHs accordingly
+<code>
+/share/apps/CENTOS7/flye/2.9.1/bin/flye --version
+.9.1-b1780
+</code>
+  * v2.9 (August 2021)
+  * python bin/flye
+<code>
+export PATH=/share/apps/CENTOS7/flye/2.9/bin:$PATH
+export LD_LIBRARY_PATH=/share/apps/CENTOS7/flye/2.9/lib:$LD_LIBRARY_PATH
+which flye
+/share/apps/CENTOS7/flye/2.9/bin/flye
+flye --version
+.9-b1774
+</code>
   * https://github.com/fenderglass/Flye
@@ Line 638: / Line 678: @@
 Using htslib 1.9
 Copyright (C) 2018 Genome Research Ltd.
+</code>
+  * **iqtree** fcohanlab/jwang06
+<code>
+[hmeij@greentail52 ~]$ iqtree --version
+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>
@@ Line 692: / Line 754: @@
 ====== OpenHPC ======
-So I remember where I put the repos ''/share/apps/src/greentail52/openhpc''
+So I remember where I put the tar repo file
-  * whitetail tar ball for centos7/warewulf (no slurm)
+  * OpenHPC v2.4
-  * http://repos.openhpc.community/OpenHPC/2.0RC1/CentOS_8/x86_64/
+  * Rocky 8.5
-  * http://repos.openhpc.community/ohpc-1.3/1.3.9/base/CentOS_7/x86_64/
+  * Slurm 20.11.8
-  * https://github.com/warewulf/warewulf3 (master git zip file)
+  * Warewulf 3.9
+  * x86_64
+<code>
+[root@cottontail2 ~]# ll /share/apps/src/cottontail2/openhpc/
+total 8290421
+-rw------- 1 root root     562276 Mar 17 09:34 Install_guide-Rocky8-Warewulf-SLURM-2.4-x86_64.pdf
+-rw-r--r-- 1 root root      10720 Mar 17 09:35 ohpc-release-2-1.el8.x86_64.rpm
+-rw-r--r-- 1 root root 8531681280 Mar 17 09:33 OpenHPC-2.4.EL_8.x86_64.tar
+</code>
 ====== OneAPI ======
@@ Line 908: / Line 981: @@
 </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>
+  * **PCAngsd**, requires miniconda3's python
+  * https://github.com/Rosemeis/pcangsd
+  * apparently the repo is needed ''/share/apps/CENTOS7/pcangsd/1.1.0''
+<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>
@@ Line 1267: / Line 1396: @@
 cufflinks                 2.2.1                    py27_2    bioconda
 samtools                  1.13                 h8c37831_0
+# fcohan lab
+[hmeij@petaltail ~]$ iqtree --version
+IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021
 </code>
 **Trinity** assembles transcript sequences from Illumina RNA-Seq data.
@@ Line 3158: / Line 3293: @@
 ====== Amber ======
+** Amber 22 **
+Details on how to run on CentOS7 can be found at
+  * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#amber22
 ** Amber 20 **

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