cluster:73
Differences
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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cluster:73 [2019/07/17 17:22] hmeij07 [OpenStructure] |
cluster:73 [2019/09/24 12:08] hmeij07 [R & R/parallel] |
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| Line 43: | Line 43: | ||
| # setup the environment | # setup the environment | ||
| - | `egrep ^export / | + | egrep ^export / |
| ost --help | ost --help | ||
| Line 55: | Line 55: | ||
| </ | </ | ||
| + | |||
| + | Remarkably complex compilations. | ||
| + | |||
| ====== PyCharm EDU ====== | ====== PyCharm EDU ====== | ||
| Line 70: | Line 73: | ||
| * add the bin/ directory to your PATH (see examples on this page) | * add the bin/ directory to your PATH (see examples on this page) | ||
| * http:// | * http:// | ||
| + | |||
| + | ====== Spyder ====== | ||
| + | |||
| + | * Spyder: The Scientific Python Development Environment | ||
| + | * https:// | ||
| + | * See Python 3.5.2 for more details | ||
| ====== Python3 ====== | ====== Python3 ====== | ||
| - | --- // | + | Added to both 3.5.2 versions\\ |
| + | '' | ||
| + | --- // | ||
| - | Added to both python versions 3.5.2 and 3.5.2-mpi the following modules all needed for Spyder. | + | < |
| + | Successfully installed | ||
| + | Send2Trash-1.5.0 | ||
| + | ipywidgets-7.5.0 | ||
| + | jupyter-1.0.0 | ||
| + | jupyter-client-5.3.1 | ||
| + | jupyter-console-6.0.0 | ||
| + | notebook-6.0.0 | ||
| + | prometheus-client-0.7.1 | ||
| + | terminado-0.8.2 | ||
| + | widgetsnbextension-3.5.0 | ||
| + | json5-0.8.5 | ||
| + | jupyterlab-1.0.2 | ||
| + | jupyterlab-server-1.0.0 | ||
| + | tornado-6.0.3 | ||
| + | </ | ||
| + | |||
| + | |||
| + | |||
| + | Added to both python versions 3.5.2 and 3.5.2-mpi the following modules all needed for Spyder.\\ | ||
| + | --- // | ||
| - | * Spyder: The Scientific Python Development Environment | ||
| - | * https:// | ||
| < | < | ||
| Line 232: | Line 261: | ||
| * www: http:// | * www: http:// | ||
| - | ====== Kallisto & Trinity ====== | + | ====== Kallisto & Trinity |
| + | |||
| + | **FastQC** A quality control tool for high throughput sequence data. | ||
| + | |||
| + | * '' | ||
| + | * location: / | ||
| + | * https:// | ||
| **kallisto** is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | **kallisto** is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | ||
| Line 348: | Line 384: | ||
| </ | </ | ||
| + | |||
| + | |||
| Line 1787: | Line 1825: | ||
| ====== R & R/parallel ====== | ====== R & R/parallel ====== | ||
| + | * R 3.6.1 (running against " | ||
| + | * New java jdk-12.0.2 (by default in your path) | ||
| + | * packages lme4 and tidyverse installed (dependencies=TRUE) | ||
| + | * https:// | ||
| + | * packages: mice, rpart, party, caret, randomforest, | ||
| + | * note: had to make a link to omp.h from gcc 4.8.4 to OS native gcc...works? | ||
| + | |||
| + | < | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | #export PATH=/ | ||
| + | #export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | </ | ||
| * R 3.5.1 (new libcurl package) | * R 3.5.1 (new libcurl package) | ||
| - | * Uses same old java home 1.7.0_21, should remember to update | + | * Uses same old java home 1.7.0_21 |
| * package lme4 installed | * package lme4 installed | ||
| Line 1798: | Line 1856: | ||
| export PATH=/ | export PATH=/ | ||
| export LD_LIBRARY_PATH=/ | export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| </ | </ | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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