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cluster:73 [2019/07/17 17:23] hmeij07 [OpenStructure] |
cluster:73 [2020/01/14 14:40] hmeij07 [Paleogenomics Tools] |
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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. | ||
+ | |||
+ | ====== Paleogenomics Tools ====== | ||
+ | |||
+ | Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: | ||
+ | |||
+ | * Samtools: Reading/ | ||
+ | * BCFtools: | ||
+ | * HTSlib: A C library for reading/ | ||
+ | |||
+ | < | ||
+ | |||
+ | # add to environment | ||
+ | export PATH=/ | ||
+ | export PATH=/ | ||
+ | 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 ====== | ====== OpenStructure ====== | ||
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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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</ | </ | ||
+ | |||
+ | |||
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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, 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 | ||
< | < |