cluster:73
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cluster:73 [2023/07/04 12:24] hmeij07 [Sequencing Tools #3] |
cluster:73 [2023/08/21 13:41] hmeij07 [Masurca] |
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| + | |||
| + | ====== Miniconda3-py311 ====== | ||
| + | |||
| + | ====== Masurca ====== | ||
| + | |||
| + | |||
| + | * module: masurca/ | ||
| + | * https:// | ||
| + | * supports openmp (maybe) | ||
| + | * queues mwgpu, exx96 (centos 7) | ||
| + | |||
| + | |||
| + | < | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | |||
| + | [hmeij@cottontail2 ~]$ masurca --version | ||
| + | version 4.1.0 | ||
| + | |||
| + | |||
| + | </ | ||
| ====== Trimmomatic ====== | ====== Trimmomatic ====== | ||
| Line 348: | Line 371: | ||
| Somewhat annoying, no miniconda3 package, (python 3.9, gcc 9.2). Local building (without installation) on centos7 greentail52. | Somewhat annoying, no miniconda3 package, (python 3.9, gcc 9.2). Local building (without installation) on centos7 greentail52. | ||
| + | * setup env as for all packages in #3, see top of section | ||
| * v2.9.2 (June 2023) | * v2.9.2 (June 2023) | ||
| * python bin/flye | * python bin/flye | ||
| - | * chnage | + | * change |
| < | < | ||
| Line 415: | Line 439: | ||
| </ | </ | ||
| + | |||
| + | ** BBmap ** | ||
| + | |||
| + | * location: / | ||
| + | * java programs | ||
| + | * https:// | ||
| ====== Galario CPU+GPU ====== | ====== Galario CPU+GPU ====== | ||
| Line 766: | Line 796: | ||
| * git clone https:// | * git clone https:// | ||
| * python ./setup.py install | * python ./setup.py install | ||
| - | * requires CentOS7 so queues mwgpu, amber128 and exx96 | + | * requires CentOS7 so queues mwgpu, |
| * or for debugging use greentail52 | * or for debugging use greentail52 | ||
| * / | * / | ||
| Line 1091: | Line 1121: | ||
| pcangsd --version | pcangsd --version | ||
| pcangsd 1.10 | pcangsd 1.10 | ||
| + | |||
| + | </ | ||
| + | |||
| + | * **angsd**, requires miniconda3, same environment as pcangsd | ||
| + | * http:// | ||
| + | * add location of angsd to PATH env | ||
| + | |||
| + | < | ||
| + | |||
| + | $ pwd | ||
| + | / | ||
| + | |||
| + | $ ls -l angsd | ||
| + | -rwxr-xr-x 1 hmeij its 5517248 Jul 6 14:11 angsd | ||
| + | |||
| + | $ ./ | ||
| + | -> angsd version: 0.940-dirty (htslib: 1.16) build(Jul | ||
| </ | </ | ||
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07
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