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cluster:73 [2022/04/25 14:52]
hmeij07 [Paleogenomics Tools]
cluster:73 [2022/11/07 13:59] (current)
hmeij07 [Miniconda3]
Line 223: Line 223:
 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 233: 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 244: 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>
Line 319: Line 327:
 ** Flye ** ** Flye **
  
-Somewhat annoying, no miniconda3 package, so local install, use minconda3 env+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+  * v2.9 (August 2021)
   * python bin/flye   * python bin/flye
  
Line 659: Line 678:
 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>
Line 966: Line 1007:
   * **PCAngsd**, requires miniconda3's python   * **PCAngsd**, requires miniconda3's python
   * https://github.com/Rosemeis/pcangsd   * https://github.com/Rosemeis/pcangsd
 +  * apparently the repo is needed ''/share/apps/CENTOS7/pcangsd/1.1.0''
  
 <code> <code>
Line 1354: 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 3245: 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/73.1650912765.txt.gz · Last modified: 2022/04/25 14:52 by hmeij07