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cluster:73 [2022/04/01 10:09]
hmeij07 [Paleogenomics Tools]
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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 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 228: 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
Line 239: Line 244:
 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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   * https://github.com/ginolhac/mapDamage/issues/25   * https://github.com/ginolhac/mapDamage/issues/25
   * docker container is broke   * docker container is broke
-  * requires centos6 so queues hp12, mw128+  * requires centos6 so queues hp12, mw128  .. may run elsewhere?
   * conda install -c 'bioconda' mapdamage2   * conda install -c 'bioconda' mapdamage2
  
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   seqtk              bioconda/linux-64::seqtk-1.3-h5bf99c6_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> </code>
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 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 3190: 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/73.1648822142.txt.gz ยท Last modified: 2022/04/01 10:09 by hmeij07