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cluster:73 [2019/10/02 14:31] hmeij07 [OpenStructure] |
cluster:73 [2020/01/14 15:07] 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: | ||
+ | |||
+ | * 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 ====== | ||
Line 1844: | Line 1884: | ||
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=/ | ||
Line 2377: | Line 2417: | ||
* 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 | ||
< | < |