cluster:73
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cluster:73 [2019/07/17 17:12] hmeij07 [Python2] |
cluster:73 [2019/08/27 13:31] hmeij07 [Kallisto & Trinity] |
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| The list of software was primarily compiled under RHEL5.1 but more recent compilation are done on host sharptail under RHEL5.5. Newer compilations are done with CentOS 6.5 (since summer 2013) on either swallowtail or node n33. | The list of software was primarily compiled under RHEL5.1 but more recent compilation are done on host sharptail under RHEL5.5. Newer compilations are done with CentOS 6.5 (since summer 2013) on either swallowtail or node n33. | ||
| + | |||
| + | ====== OpenStructure ====== | ||
| + | |||
| + | Open-Source Computational Structural Biology Framework | ||
| + | |||
| + | * v 1.9 | ||
| + | * https:// | ||
| + | * recipe at / | ||
| + | |||
| + | OpenStructure relies on these applications and Python 2.7.15 (see python2 section). | ||
| + | |||
| + | < | ||
| + | |||
| + | -- Boost version: 1.68.0 | ||
| + | -- Found the following Boost libraries: | ||
| + | -- | ||
| + | -- | ||
| + | -- | ||
| + | -- | ||
| + | -- | ||
| + | -- | ||
| + | -- regex | ||
| + | -- | ||
| + | -- Found ZLIB: / | ||
| + | -- Found PNG: / | ||
| + | -- Found EIGEN: / | ||
| + | -- Numpy headers found | ||
| + | -- Found FFTW: / | ||
| + | -- Found TIFF: / | ||
| + | |||
| + | |||
| + | # setup the environment | ||
| + | egrep ^export / | ||
| + | |||
| + | ost --help | ||
| + | Usage: | ||
| + | |||
| + | ost [ost options] [script to execute] [script parameters] | ||
| + | |||
| + | or | ||
| + | ost [action name] [action options] | ||
| + | |||
| + | |||
| + | </ | ||
| + | |||
| + | Remarkably complex compilations. | ||
| + | |||
| ====== PyCharm EDU ====== | ====== PyCharm EDU ====== | ||
| Line 26: | 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 188: | Line 261: | ||
| * www: http:// | * www: http:// | ||
| - | ====== Kallisto & Trinity ====== | + | ====== Kallisto & Trinity |
| **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 305: | Line 378: | ||
| </ | </ | ||
| + | |||
| + | **FastQC** A quality control tool for high throughput sequence data. | ||
| + | |||
| + | * '' | ||
| + | * location: / | ||
| + | * https:// | ||
| ====== Sequencing Tools ====== | ====== Sequencing Tools ====== | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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