Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Here are a few tips for Pavian to work with large data.
This post introduces how to complie latest R for RStidio, and install RStudio Server in a Debian host.
While installing the R package “hdf5r” version 1.3.3, I encountered the error:
fatal error: hdf5.h: No such file or directory
#include <hdf5.h>
^~~~~~~~
compilation terminated.
My OS is Debian buster/10.6, and the package “libhdf5-dev” has been installed. It looks R cannot find the path of hdf5 header and library files.
Viewing and annotation of a huge phylogenetic tree, especially with hundreds or even thousamds taxa, is always a problem. This post provides a method to split a phylogenetic tree into multiple pages of a PDF file by pdfposter.
Conda is quite convenient for non-root users to install softwares in Linux system. But sometimes there is no packages available in anaconda repository and we have to install these softwares from source. This post introduces the way to compile and install softwares from source, use the Kyoto Cabinet Perl module as an example.
BEAST (and BEAST 2, of course) is widely uesed for phylogenetic inference. But it is quite complicated. This post represents some useful tips while using BEAST.
Install NVidia driver in Linux server is always tedious and painful. Fortunatelly, Debian stable/Stretch provids ready-to-use NVidia drivers and CUDA toolkits. This post indicates the proper way to install up-to-date Nvidia driver and CUDA in Debian way.