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cluster:73 [2019/07/09 14:57] hmeij07 [Python3] |
cluster:73 [2019/09/23 12:05] hmeij07 [R & R/parallel] |
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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 ====== | ||
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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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</ | </ | ||
+ | |||
+ | |||
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====== 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(does not exist), randomforest, | ||
+ | |||
+ | < | ||
+ | |||
+ | 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 | ||
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export PATH=/ | export PATH=/ | ||
export LD_LIBRARY_PATH=/ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
</ | </ | ||
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====== Python2 ====== | ====== Python2 ====== | ||
- | Note 2.7 branch is end of life 01/10/2020 | + | **Note 2.7 branch is end of life 01/01/2020** |
Note: since the latest update to CentOS 6.10 the native python in the OS is / | Note: since the latest update to CentOS 6.10 the native python in the OS is / | ||
+ | |||
+ | |||
+ | * Python 2.7.15 | ||
+ | * compile with enable-share | ||
+ | * numpy and scipy packages | ||
+ | |||
+ | < | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | </ | ||