Software

While using ZDOCK in Debian 11, an error message shew:

$ ./mark_sur
./mark_sur: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory

yt-dlp is a youtube-dl fork and able to download videos and audios from many streaming platforms, such as YouTube.

This blog describes installation in Debian bullseye and some common usage examples.

MrBayes 3 is a program for Bayesian inference and model choice across a large space of phylogenetic and evolutionary models. And BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. BEAGLE is able to accelerate MrBayes analyses very much.

This post introduces the way to run MrBayes along with BEAGLE.

Due to the limited space of EndNote online, I still used to sync EndNote libraries through OneNote. The drawback is, the library might be corrupted occasionally (about once a couple of months).

I have introduced how to install R and RStudio Server before. But free version of RStudio Server lack of many security features, especially SSL.

This post introduces to secure RStudio Server by an Nginx reverse proxy.

This post was first released at 2019-05-26, and updated at 2021-04-20.

Since PyMOL 2.x released, there were no binary installer avaliable for Windows.

PyMOL Wiki provides the way to install open source PyMOL in Windows under Python 3.x.

This post provided the method to install PyMOL 2.x by conda (Anaconda or Minoconda) in Windows.

BEAGLE is a high-performance library to accelerate the calculations of Bayesian and Maximun Likelihood phylogenetics analyses. The latest version of beagle-lib was released on Dec 4, 2018.

When compiled for NVidia Tesla V100 on Debian buster 10.9, an error was encountered:

nvcc fatal   : Value 'compute_30' is not defined for option 'gpu-architecture'

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.