cluster:73
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
cluster:73 [2019/08/27 13:33] hmeij07 [Kallisto & Trinity & FastQC] |
cluster:73 [2020/01/30 13:06] hmeij07 |
||
|---|---|---|---|
| Line 2: | Line 2: | ||
| **[[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 / | ||
| Line 10: | Line 10: | ||
| 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 ====== | ====== OpenStructure ====== | ||
| Line 1825: | Line 1876: | ||
| ====== 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 1836: | Line 1907: | ||
| export PATH=/ | export PATH=/ | ||
| export LD_LIBRARY_PATH=/ | export LD_LIBRARY_PATH=/ | ||
| + | |||
| + | export PATH=/ | ||
| + | export LD_LIBRARY_PATH=/ | ||
| </ | </ | ||
| Line 2346: | Line 2420: | ||
| * 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
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
