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cluster:73 [2022/01/03 14:39]
hmeij07 [Miniconda3]
cluster:73 [2022/11/07 13:59] (current)
hmeij07 [Miniconda3]
Line 3: Line 3:
  
 ====== Software ====== ====== 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'' 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''
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 Some compilations require 7.x and are in /share/apps/CENTOS7 \\ Some compilations require 7.x and are in /share/apps/CENTOS7 \\
  
 +
 +====== HPC SDK ======
 +
 +    * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:212
 +    * Nvidia SDK v 22.2
  
 ====== Magenta ====== ====== Magenta ======
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 Suite of tools for high-accuracy basecaling, assembly, polishing, and alignment. Installed in a specific miniconda3 environment (see below). 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     * debug server greentail52
   * PREFIX=/share/apps/CENTOS7/miniconda3   * PREFIX=/share/apps/CENTOS7/miniconda3
Line 223: Line 233:
 <code> <code>
  
-# environment+# environment for all modules
 source /share/apps/CENTOS7/miniconda3/etc/profile.d/conda.sh source /share/apps/CENTOS7/miniconda3/etc/profile.d/conda.sh
 export PATH=/share/apps/CENTOS7/miniconda3/bin:$PATH export PATH=/share/apps/CENTOS7/miniconda3/bin:$PATH
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 which conda python pip mpirun gcc cmake which conda python pip mpirun gcc cmake
 python --version 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> </code>
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 ** Flye ** ** 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
 +2.9.1-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
 +2.9-b1774
 +
 +</code>
  
   * https://github.com/fenderglass/Flye    * https://github.com/fenderglass/Flye 
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 Using htslib 1.9 Using htslib 1.9
 Copyright (C) 2018 Genome Research Ltd. 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> </code>
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 ====== OpenHPC ====== ====== 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.
-  * 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 ====== ====== OneAPI ======
Line 903: Line 981:
 </code> </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
 +2.0.6
 +
 +</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 1262: Line 1396:
 cufflinks                 2.2.1                    py27_2    bioconda cufflinks                 2.2.1                    py27_2    bioconda
 samtools                  1.13                 h8c37831_0     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> </code>
 +
 +
  
 **Trinity** assembles transcript sequences from Illumina RNA-Seq data. **Trinity** assembles transcript sequences from Illumina RNA-Seq data.
Line 2997: Line 3137:
   * https://edwards.sdsu.edu/research/c11-on-centos-6/   * https://edwards.sdsu.edu/research/c11-on-centos-6/
     * C11++ on CentOS6, two version of gcc     * C11++ on CentOS6, two version of gcc
-    * read the R-3.6.1_configure file in ''/share/apps/src/cottontail2''+    * read the R-3.6.1_configure file in ''/share/apps/CENTOS6/R/R-3.6.1_configure''
  
 <code> <code>
Line 3153: Line 3293:
  
 ====== Amber ======  ====== 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 ** ** Amber 20 **
cluster/73.1641238755.txt.gz · Last modified: 2022/01/03 14:39 by hmeij07