cluster:73
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cluster:73 [2022/04/01 10:13] hmeij07 [Paleogenomics Tools] |
cluster:73 [2022/11/07 13:57] hmeij07 [Miniconda3] |
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| ====== 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 218: | 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 228: | Line 233: | ||
| < | < | ||
| - | # environment | + | # environment |
| source / | source / | ||
| export PATH=/ | export PATH=/ | ||
| Line 239: | Line 244: | ||
| which conda python pip mpirun gcc cmake | which conda python pip mpirun gcc cmake | ||
| python --version | python --version | ||
| + | |||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | / | ||
| + | |||
| </ | </ | ||
| Line 313: | 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 639: | Line 679: | ||
| 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 | ||
| + | |||
| + | # https:// | ||
| + | # calterlab, annika | ||
| + | |||
| + | 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 | ||
| </ | </ | ||
| Line 922: | Line 978: | ||
| * https:// | * https:// | ||
| * 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 ' | * conda install -c ' | ||
| Line 940: | Line 996: | ||
| [hmeij@petaltail ~]$ mapDamage --version | [hmeij@petaltail ~]$ mapDamage --version | ||
| 2.0.6 | 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 1301: | Line 1390: | ||
| 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 3192: | Line 3287: | ||
| ====== Amber ====== | ====== Amber ====== | ||
| + | |||
| + | ** Amber 22 ** | ||
| + | |||
| + | Details on how to run on CentOS7 can be found at | ||
| + | |||
| + | * https:// | ||
| ** Amber 20 ** | ** Amber 20 ** | ||
cluster/73.txt ยท Last modified: 2024/02/16 11:17 by hmeij07
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