cluster:73
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
cluster:73 [2022/01/03 14:39] hmeij07 [Miniconda3] |
cluster:73 [2022/10/18 09:23] hmeij07 [Sequencing Tools #3] |
||
|---|---|---|---|
| Line 3: | Line 3: | ||
| ====== Software ====== | ====== Software ====== | ||
| + | |||
| + | [[cluster: | ||
| + | |||
| + | 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** ''/ | IMPORTANT NOTE: **Since moving to the TrueNAS/ZFS appliance all references to** ''/ | ||
| Line 19: | Line 24: | ||
| Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
| + | |||
| + | ====== HPC SDK ====== | ||
| + | |||
| + | * https:// | ||
| + | * Nvidia SDK v 22.2 | ||
| ====== Magenta ====== | ====== Magenta ====== | ||
| Line 213: | 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, |
| * debug server greentail52 | * debug server greentail52 | ||
| * PREFIX=/ | * PREFIX=/ | ||
| Line 223: | Line 233: | ||
| < | < | ||
| - | # environment | + | # environment |
| source / | source / | ||
| export PATH=/ | export PATH=/ | ||
| Line 234: | Line 244: | ||
| which conda python pip mpirun gcc cmake | which conda python pip mpirun gcc cmake | ||
| python --version | python --version | ||
| + | |||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | |||
| </ | </ | ||
| Line 308: | Line 326: | ||
| ** 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 | ||
| + | |||
| + | < | ||
| + | |||
| + | / | ||
| + | 2.9.1-b1780 | ||
| + | |||
| + | </ | ||
| + | |||
| + | * v2.9 (August 2021) | ||
| + | * python bin/flye | ||
| + | |||
| + | < | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | which flye | ||
| + | / | ||
| + | flye --version | ||
| + | 2.9-b1774 | ||
| + | |||
| + | </ | ||
| * https:// | * https:// | ||
| Line 633: | Line 678: | ||
| Using htslib 1.9 | Using htslib 1.9 | ||
| Copyright (C) 2018 Genome Research Ltd. | Copyright (C) 2018 Genome Research Ltd. | ||
| + | |||
| + | </ | ||
| + | |||
| + | * **iqtree** fcohanlab/ | ||
| + | |||
| + | < | ||
| + | |||
| + | [hmeij@greentail52 ~]$ iqtree --version | ||
| + | IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020 | ||
| + | |||
| </ | </ | ||
| Line 687: | Line 742: | ||
| ====== OpenHPC ====== | ====== OpenHPC ====== | ||
| - | So I remember where I put the repos ''/ | + | So I remember where I put the tar repo file |
| - | * whitetail tar ball for centos7/ | + | * OpenHPC v2.4 |
| - | * http:// | + | * Rocky 8.5 |
| - | * http://repos.openhpc.community/ohpc-1.3/1.3.9/ | + | * Slurm 20.11.8 |
| - | * https://github.com/ | + | * Warewulf 3.9 |
| + | * x86_64 | ||
| + | |||
| + | < | ||
| + | |||
| + | [root@cottontail2 ~]# ll /share/apps/src/cottontail2/ | ||
| + | total 8290421 | ||
| + | -rw------- 1 root root | ||
| + | -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 969: | ||
| </ | </ | ||
| + | * **mapDamage2** | ||
| + | * https:// | ||
| + | * docker container is broke | ||
| + | * requires centos6 so queues hp12, mw128 .. may run elsewhere? | ||
| + | * conda install -c ' | ||
| + | |||
| + | |||
| + | < | ||
| + | |||
| + | # env | ||
| + | export PATH="/ | ||
| + | export LD_LIBRARY_PATH="/ | ||
| + | |||
| + | The following NEW packages will be INSTALLED: | ||
| + | |||
| + | mapdamage2 | ||
| + | pysam bioconda/ | ||
| + | seqtk bioconda/ | ||
| + | |||
| + | [hmeij@petaltail ~]$ mapDamage --version | ||
| + | 2.0.6 | ||
| + | |||
| + | </ | ||
| + | |||
| + | * **PCAngsd**, | ||
| + | * https:// | ||
| + | * apparently the repo is needed ''/ | ||
| + | |||
| + | < | ||
| + | |||
| + | source / | ||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | which pcangsd | ||
| + | / | ||
| + | pcangsd --version | ||
| + | pcangsd 1.10 | ||
| + | |||
| + | </ | ||
| + | |||
| + | * **Standard RAxML version** | ||
| + | * https:// | ||
| + | |||
| + | < | ||
| + | |||
| + | # add path to $PATH | ||
| + | |||
| + | [hmeij@greentail52 tmp]$ ll / | ||
| + | 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 | ||
| + | |||
| + | </ | ||
| Line 1262: | Line 1384: | ||
| cufflinks | cufflinks | ||
| samtools | samtools | ||
| + | |||
| + | # fcohan lab | ||
| + | [hmeij@petaltail ~]$ iqtree --version | ||
| + | IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021 | ||
| </ | </ | ||
| + | |||
| + | |||
| **Trinity** assembles transcript sequences from Illumina RNA-Seq data. | **Trinity** assembles transcript sequences from Illumina RNA-Seq data. | ||
| Line 2997: | Line 3125: | ||
| * https:// | * https:// | ||
| * C11++ on CentOS6, two version of gcc | * C11++ on CentOS6, two version of gcc | ||
| - | * read the R-3.6.1_configure file in ''/ | + | * read the R-3.6.1_configure file in ''/ |
| < | < | ||
| Line 3153: | Line 3281: | ||
| ====== Amber ====== | ====== Amber ====== | ||
| + | |||
| + | ** Amber 22 ** | ||
| + | |||
| + | Details on how to run on CentOS7 can be found at | ||
| + | |||
| + | * https:// | ||
| ** Amber 20 ** | ** Amber 20 ** | ||
cluster/73.txt · Last modified: 2024/02/16 11:17 by hmeij07
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
