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cluster:73 [2023/06/27 20:41] hmeij07 [Matlab] |
cluster:73 [2023/07/13 15:29] hmeij07 [pytraj] |
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+ | |||
+ | ====== 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 ====== | ||
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** Flye ** | ** Flye ** | ||
- | Somewhat annoying, no miniconda3 package, | + | 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 |
< | < | ||
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</ | </ | ||
- | * https:// | ||
- | * miniconda3 | ||
- | * De novo assembler for single molecule sequencing reads using repeat graphs | ||
- | * v2.8.3 | ||
- | < | ||
- | |||
- | # To activate this environment, | ||
- | # $ conda activate flye | ||
- | # To deactivate an active environment, | ||
- | # $ conda deactivate | ||
- | |||
- | </ | ||
** Filtlong ** | ** Filtlong ** | ||
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* 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 | ||
* / | * / | ||
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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 | ||
</ | </ |