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cluster:73 [2022/06/28 11:37]
hmeij07 [Kallisto & Trinity & FastQC] 		cluster:73 [2023/02/10 09:52]
hmeij07 [OpenHPC]
Line 23: Line 23:
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\ on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\ Some compilations require 7.x and are in /share/apps/CENTOS7 \\
 +
 +
 +
 +====== Trimmomatic ======
 +
 +  * http://www.usadellab.org/cms/?page=trimmomatic
 +  * binary download and stage
 +  * java -jar trimmomatic-0.39.jar ...
 +
 +<code>
 +
 +/share/apps/CENTOS6/Trimmomatic-0.39/
 +[root@cottontail Trimmomatic-0.39]# ll
 +total 176
 +drwxr-xr-x 2 root root      8 Apr  8  2019 adapters
 +-rw-r--r-- 1 root root  35147 May 16  2018 LICENSE
 +-rw-r--r-- 1 root root 128502 Apr  8  2019 trimmomatic-0.39.jar
 +
 +</code>
  
  
Line 223: Line 242:
 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 252:
 <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 263:
 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 346:
 ** 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 697:
 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 728: Line 788:
 -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      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 -rw-r--r-- 1 root root 8531681280 Mar 17 09:33 OpenHPC-2.4.EL_8.x86_64.tar
 +
 +
 +
 +# this is all that is needed for ohpc base compute client
 +# see the recipe for cct2 and follow compute node only ingredients
 +
 +[root@cottontail2 ~]# ll /share/apps/src/cottontail2/ohpc-compute/
 +total 95196
 +-rw-r--r-- 1 root root  2696360 Feb 10 09:21 hwloc-ohpc-2.7.0-3.9.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root   266252 Feb 10 09:22 lmod-ohpc-8.7.6-12.3.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root     7268 Feb 10 09:22 ohpc-base-compute-2.6.1-5.1.ohpc.2.6.1.x86_64.rpm
 +-rw-r--r-- 1 root root     8204 Feb 10 09:23 ohpc-filesystem-2.6-2.3.ohpc.2.6.noarch.rpm
 +-rw-r--r-- 1 root root    10720 Feb 10 09:23 ohpc-release-2-1.el8.x86_64.rpm
 +-rw-r--r-- 1 root root     7124 Feb 10 09:27 ohpc-slurm-client-2.6.1-5.1.ohpc.2.6.1.x86_64.rpm
 +-rw-r--r-- 1 root root 74326532 Feb 10 09:23 singularity-ohpc-3.7.1-5.1.ohpc.2.1.x86_64.rpm
 +-rw-r--r-- 1 root root    22168 Feb 10 09:24 slurm-contribs-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root   247392 Feb 10 09:24 slurm-example-configs-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root 18764472 Feb 10 09:24 slurm-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root   176480 Feb 10 09:28 slurm-pam_slurm-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
 +-rw-r--r-- 1 root root   785112 Feb 10 09:25 slurm-slurmd-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm
  
 </code> </code>
Line 3252: Line 3332:
  
 ====== 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.txt · Last modified: 2024/05/15 08:58 by hmeij07

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