cluster:73
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cluster:73 [2019/07/23 13:04] hmeij07 [Python3] |
cluster:73 [2020/01/14 14:29] 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/ | ||
| + | |||
| + | < | ||
| + | |||
| + | | ||
| + | |||
| + | </ | ||
| + | |||
| + | ====== 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 ====== | ||
| Line 82: | Line 104: | ||
| ====== Python3 ====== | ====== Python3 ====== | ||
| - | Added to both 3.5.2 versions | + | Added to both 3.5.2 versions\\ |
| + | '' | ||
| --- // | --- // | ||
| Line 96: | Line 119: | ||
| terminado-0.8.2 | terminado-0.8.2 | ||
| widgetsnbextension-3.5.0 | 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. | + | |
| + | Added to both python versions 3.5.2 and 3.5.2-mpi the following modules all needed for Spyder.\\ | ||
| + | --- // | ||
| Line 255: | Line 283: | ||
| * 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. | ||
| Line 371: | Line 406: | ||
| </ | </ | ||
| + | |||
| + | |||
| Line 1810: | Line 1847: | ||
| ====== 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 | ||
| Line 1821: | Line 1878: | ||
| 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 | ||
| < | < | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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