Problem:
You want to read alignment matrices like BLOSUM62 in the QUASAR format. The solution needs to be integrable into C++ code easily.
02
Nov
2013
24
Oct
2013
A simple tool for FASTA statistics
The issue
It is surprisingly difficult to compute simple statistics of FASTA files using existing software. I recently needed to compute the nucleotide count and relative GC frequency of a single sequence in FASTA format, but unless you install dependency-heavy native software like FASTX or you develop it by yourself using BioPython or similar, there doesn’t seem to be a simple, dependency-free solution for this simple set of problem.
22
Oct
2013
Docker: Remove all images and containers
Problem:
You use Docker, but working with it created lots of images and containers. You want to remove all of them to save disk space.
09
Oct
2013
Java FX: How to set the column constraint property using FXML
Problem:
You have a Java FXML file document with a TableView and want to set the columnResizePolicy of this TableView in the fxml document.
21
Aug
2013
A simple mmap() readonly example
Problem:
You want to use mmap() from sys/stat.h POSIX header to map a file for reading (not writing). You can’t find any simple bare example on the internet.
21
Aug
2013
How to get filesize using stat() in C/C++
Problem:
You want to use stat() from sys/stat.h POSIX header in order to get the size of a file.
21
Aug
2013
How to check if file exists using stat
Problem:
You want to use stat() from sys/stat.h POSIX header to check if a file with a given name exists.
08
Aug
2013
How to create msgpack DEB packages
Problem:
You want to create a binary DEB package of the msgpack C++ binding. However, there is no official DEB package available.
01
Aug
2013
Checking if Hugepages are enabled in Linux
Problem:
On your Linux system, you want to check whether transparent hugepages are enabled on your system.
Solution:
It’s pretty simple:
cat /sys/kernel/mm/transparent_hugepage/enabledYou will get an output like this:
always [madvise] neverYou’ll see a list of all possible options ( always, madvise, never ), with the currently active option being enclosed in brackets.madvise is the default.
01
Aug
2013
How to build libsodium (NaCl) DEB packages
Problem:
You want to create a binary DEB package of libsodium. However, there is no official DEB package available for the latest version.
09
Jul
2013
User Mode Linux for Beginners – Setup and first VM
Why another UML tutorial?
This is not the first tutorial on UML — there are hundreds of them publicly available on the internet. However, none of them seems to fulfill my requirements:
- All my computers and servers (= UML hosts) run on x86_64, not on i386.
- Use an up-to date (self-compiled) UML version, so you can use the latest features
- One simple set of scripts. Execute them in the correct order to get it up and running – no config file editing etc.
- Root should not be required (disregarding debootstrap) —> No /mnt mounts or similar
- No nasty filesystem image that eats up space on the host and limits resources on the UML VM. HostFS eliminates all those disadvantages – if you want to limit VM space, use quotas.
- No global state (e.g. mounting sth into /mnt), you should get another VM up and running concurrently by executing the setup scripts in another directory.
- Step-by-step instructions, as automated and portable as possible, but still made to be read by humans.
- No expansive techtalk. There are reference documentations out there for techtalk. A tutorial should tell you how to get it working, not why it works.
05
Apr
2013
How to use mkdir() from sys/stat.h
Problem:
You want to use the mkdir() function from the sys/stat.h POSIX header, but you don’t know what the mode_t argument should look like.
02
Apr
2013
Building LevelDB Debian (.deb) packages
Problem:
You intend to install LevelDB, but you don’t want to manually install & compile it as described here.
Instead, you just want to use the debian packaging system and some reproducible method of creating a DEB package from LevelDB.
Reasons for preferring not to compile & install manually could be:
- You want to deploy LevelDB to one ore more environments that don’t have a complete build environment
- You prefer a clean install-uninstall-purge package lifetime management
- You need a reproducible process to deploy LevelDB
31
Mar
2013
mmap with Boost IOStreams: A minimalist’s example
The following C++ program uses boost::iostreams to memory-map a file, read it’s content into a std::string and print it to cout.
It provides a minimal example of how to use the boost::iostreams portable mmap functionality.
//Compile like this: g++ -o mmap mmap.cpp -lboost_iostreams
#include <boost/iostreams/device/mapped_file.hpp>
#include <iostream>
#include <string>
using namespace std;
using namespace boost::iostreams;
int main(int argc, char** argv) {
//Initialize the memory-mapped file
mapped_file_source file(argv[1]);
//Read the entire file into a string
string fileContent(file.data(), file.size());
//Print the string
cout << fileContent;
//Cleanup
file.close();
}Also see A simple mmap() readonly example
29
Mar
2013
Reading TAR files in C++
This article describes a method of reading TAR archives (including .tar.gz and .tar.bz2) in C++ using Boost IOStreams.
You could use libtar for this, but the original version hasn’t been updated since 2003 and doesn’t provide you flexibility and insight to the internal structure of a TAR archive. Continue reading →
16
Mar
2013
ffmpeg / avconv : List supported codecs
You can list all codecs supported by libavconv (the library used by ffmpeg / avconv) by using this command:
ffmpeg -codecsIf you don’t have the ffmpeg executable simply use
avconv -codecsNote that avconv and ffmpeg are essentially the same, but the projects split at some time and then re-merged. Starting from Ubuntu 15.04, ffmpeg is available in the repositories again, whereas previously, ffmpeg was replaced by avconv.
For details, see this StackOverflow thread and this detailed post about the ffmpeg/libav situation.
15
Mar
2013
Simple C++ HTTP download using libcurl easy API
Problem
Using the libcurl easy API you want to download a file using HTTP GET. No extended features such as authentication shall be used.
The download result shall be stored in a std::string
09
Mar
2013
How to fix ADB “error: insufficient permissions for device”
Problem:
Why trying to access your Android device using ADB, you encounter the following error:
error: insufficient permissions for device 28
Feb
2013
How to fix “Cannot find crt1.o” on Ubuntu
Problem:
You’re trying to compile something (e.g. using GCC) on Ubuntu, but you get an error message similar to this one:
/usr/bin/ld: error: cannot open crt1.o: No such file or directory /usr/bin/ld: error: cannot open crti.o: No such file or directory /usr/bin/ld: error: cannot open crtn.o: No such file or directory
17
Feb
2013
How to compile and install LLVM Gold plugin (LLVMgold.so) on Linux
Problem:
You want to use the LLVM Gold linker plugin but LLVMgold.so can’t be found.