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cluster:73 [2022/04/25 18:29] hmeij07 [Paleogenomics Tools] |
cluster:73 [2022/11/07 18:57] hmeij07 [Miniconda3] |
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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=/ | ||
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< | < | ||
- | # environment | + | # environment |
source / | source / | ||
export PATH=/ | export PATH=/ | ||
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which conda python pip mpirun gcc cmake | which conda python pip mpirun gcc cmake | ||
python --version | python --version | ||
+ | |||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
</ | </ | ||
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** Flye ** | ** Flye ** | ||
- | Somewhat annoying, no miniconda3 package, so local install, use minconda3 | + | Somewhat annoying, no miniconda3 package, so local install, use minconda3 |
+ | |||
+ | * v2.9.1 (October 2022) | ||
+ | * python bin/flye | ||
+ | * change the PATHs accordingly | ||
+ | |||
+ | < | ||
+ | |||
+ | / | ||
+ | 2.9.1-b1780 | ||
+ | |||
+ | </ | ||
- | * v2.9 | + | * v2.9 (August 2021) |
* python bin/flye | * python bin/flye | ||
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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 964: | Line 999: | ||
</ | </ | ||
- | * PCAngsd, requires miniconda3' | + | |
+ | * https:// | ||
+ | * apparently the repo is needed ''/ | ||
< | < | ||
Line 979: | Line 1016: | ||
</ | </ | ||
+ | * **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 | ||
+ | |||
+ | </ | ||
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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. | ||
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====== Amber ====== | ====== Amber ====== | ||
+ | |||
+ | ** Amber 22 ** | ||
+ | |||
+ | Details on how to run on CentOS7 can be found at | ||
+ | |||
+ | * https:// | ||
** Amber 20 ** | ** Amber 20 ** |