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cluster:73 [2019/07/17 17:12] hmeij07 [Python2] |
cluster:73 [2020/02/25 15:42] hmeij07 [R & R/parallel] |
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**[[cluster: | **[[cluster: | ||
+ | ===== Software ===== | ||
The listings below will be updated as software is installed, location is / | The listings below will be updated as software is installed, location is / | ||
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Most of the compilations have been performed by Intel' | Most of the compilations have been performed by Intel' | ||
- | The list of software was primarily compiled under RHEL5.1 but more recent compilation | + | Old compilations, |
+ | Newer compilations are done with CentOS 6.10 (since summer 2013) \\ | ||
+ | on either | ||
+ | Some compilations require 7.x and are in / | ||
+ | |||
+ | ====== Paleogenomics Tools ====== | ||
+ | |||
+ | Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: | ||
+ | |||
+ | * http:// | ||
+ | * Samtools: Reading/ | ||
+ | * BCFtools: | ||
+ | * HTSlib: A C library for reading/ | ||
+ | |||
+ | < | ||
+ | |||
+ | # add to environment | ||
+ | export PATH=/ | ||
+ | export PATH=/ | ||
+ | export PATH=/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | * https:// | ||
+ | * Program for analysing NGS data | ||
+ | |||
+ | < | ||
+ | |||
+ | # does not seem to work against htslib version above... | ||
+ | export | ||
+ | export PATH=/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | * https:// | ||
+ | * BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. | ||
+ | |||
+ | < | ||
+ | |||
+ | # with local java jre1.8.0_212 | ||
+ | export PATH=/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | ====== CD-HIT ====== | ||
+ | |||
+ | CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. | ||
+ | |||
+ | * https:// | ||
+ | * / | ||
+ | |||
+ | |||
+ | ====== 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: | ||
+ | -- | ||
+ | -- | ||
+ | -- | ||
+ | -- | ||
+ | -- | ||
+ | -- | ||
+ | -- | ||
+ | -- | ||
+ | -- 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 versions\\ |
+ | pycuda\\ | ||
+ | --- // | ||
- | Added to both python versions 3.5.2 and 3.5.2-mpi the following modules all needed for Spyder. | + | Added to both 3.5.2 versions\\ |
+ | Successfully installed\\ | ||
+ | boto-2.49.0 boto3-1.12.0 botocore-1.15.0 gensim-3.8.1 jmespath-0.9.4 s3transfer-0.3.3 smart-open-1.9.0\\ | ||
+ | joblib, scikit-learn, | ||
+ | \\ | ||
+ | Requirement already satisfied: | ||
+ | keras keras-preprocessing keras-applications\\ | ||
+ | tensorflow (requires centos7)\\ | ||
+ | --- // | ||
+ | |||
+ | |||
+ | Added to both 3.5.2 versions\\ | ||
+ | '' | ||
+ | --- // | ||
+ | |||
+ | < | ||
+ | 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 ====== | ||
+ | * https:// | ||
+ | * C11++ on CentOS6, two version of gcc | ||
+ | * read the R-3.6.1_configure file in ''/ | ||
+ | |||
+ | < | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | install.packages(' | ||
+ | </ | ||
+ | |||
+ | |||
+ | * 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 | ||
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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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* Python 2.7.15 | * Python 2.7.15 | ||
* compile with enable-share | * compile with enable-share | ||
- | * numpy and scipy packages | + | * numpy and scipy packages, and |
+ | * Successfully installed Send2Trash-1.5.0 backports-abc-0.5 futures-3.3.0 ipaddress-1.0.22 | ||
+ | * ipykernel-4.10.1 jupyter-client-5.3.4 jupyterlab-0.33.12 jupyterlab-launcher-0.11.2 | ||
+ | * notebook-5.7.8 prometheus-client-0.7.1 python-dateutil-2.8.0 singledispatch-3.4.0.3 | ||
+ | * subprocess32-3.5.4 terminado-0.8.2 tornado-5.1.1 | ||
< | < | ||
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For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, | For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, | ||
+ | |||
+ | * program: GCC v 9.2.0 | ||
+ | * / | ||
+ | * note: libgomp disabled for nanopolish compile attempt | ||
+ | |||
+ | < | ||
+ | |||
+ | wget ftp:// | ||
+ | tar zxvf gcc-9.2.0.tar.gz | ||
+ | cd gcc-9.2.0 | ||
+ | ./ | ||
+ | ./configure --prefix=/ | ||
+ | make | ||
+ | make install | ||
+ | |||
+ | |||
+ | </ | ||
* program: GCC v 4.8.4 | * program: GCC v 4.8.4 |