cluster:73
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cluster:73 [2022/04/07 10:48] hmeij07 |
cluster:73 [2022/08/03 10:38] hmeij07 [Amber] |
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| ====== Software ====== | ====== Software ====== | ||
| - | [[cluster: | + | [[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 315: | Line 318: | ||
| ** Flye ** | ** Flye ** | ||
| + | |||
| + | Somewhat annoying, no miniconda3 package, so local install, use minconda3 env | ||
| + | |||
| + | * v2.9 | ||
| + | * python bin/flye | ||
| + | |||
| + | < | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | which flye | ||
| + | / | ||
| + | flye --version | ||
| + | 2.9-b1774 | ||
| + | |||
| + | </ | ||
| * https:// | * https:// | ||
| Line 640: | Line 659: | ||
| 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 942: | Line 971: | ||
| [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 1303: | Line 1365: | ||
| 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 3194: | Line 3262: | ||
| ====== 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: 2024/05/15 08:58 by hmeij07
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