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cluster:73 [2019/07/17 17:23] hmeij07 [OpenStructure] |
cluster:73 [2019/08/27 13:33] hmeij07 [Kallisto & Trinity & FastQC] |
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# setup the environment | # setup the environment | ||
- | `egrep ^export / | + | egrep ^export / |
ost --help | ost --help | ||
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* 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:// | ||
< | < | ||
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* 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. | ||
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</ | </ | ||
+ | |||
+ | |||