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cluster:73 [2019/09/20 14:18] hmeij07 [R & R/parallel] |
cluster:73 [2020/01/14 14:27] hmeij07 [CD-HIT] |
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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 ====== | ||
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* New java jdk-12.0.2 (by default in your path) | * New java jdk-12.0.2 (by default in your path) | ||
* packages lme4 and tidyverse installed (dependencies=TRUE) | * 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? | ||
< | < | ||
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export PATH=/ | export PATH=/ | ||
export LD_LIBRARY_PATH=/ | export LD_LIBRARY_PATH=/ | ||
- | export PATH=/ | + | export PATH=/ |
- | export LD_LIBRARY_PATH=/ | + | export LD_LIBRARY_PATH=/ |
export PATH=/ | export PATH=/ | ||
export LD_LIBRARY_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 | ||
< | < |