Author Archives: Thomas Cokelaer

How to find differences between two directories using diff command

Tweet When you copy a directory with many files, you may want to check whether the copied directory is indeed an exact copy of the original. You can do that by comparing all files. You can write your own script … Continue reading

Posted in Linux | Tagged | Leave a comment

pypi upload failed due to non-existent authentication information

Tweet After trying to upload a package on Pypi website using

I got this error message:

Despite having registered and succesfully uploaded package before. What happened is that I updated my account on Pypi website by changing the … Continue reading

Posted in Uncategorized | Tagged | Leave a comment

format USB key under fedora

Tweet I created a bootable USB key and needed to format the key so that others could use it again. Using the format option (see image below) in the KDE file environment, I got this error:

I then tried … Continue reading

Posted in Linux | Tagged , | Leave a comment

All about RNA and DNA sequencing

Tweet Great entry with description of RNA and DNA sequencing: enseqlopedia

Posted in bioinformatics | Tagged , , | Leave a comment

missing SAM header with minimap2 and samtools

Tweet When using minimap2 to map sequencing reads onto a reference, you can use this kind of command (be careful, this is wrong as you will see later):

The command is verbose and prints this kind of information. Note … Continue reading

Posted in bioinformatics | Tagged , | Leave a comment

How to get pypi statistics about package download

Tweet A while ago, I designed pypiview, a Python package used to fetch the number of downloads for a package hosted on pypi website. It used to work decently but according to pypi itself the values stored are not reliable … Continue reading

Posted in Python | Tagged , , , | Leave a comment

How to prevent wget from creating duplicates

Tweet wget is used to download file from internet. For instance:

So far so good but two things may happen. First, you may interrupt the download. Second, you may load the file again. Sometimes, files are huge and you … Continue reading

Posted in Linux | Tagged | Leave a comment

Meaning of Real, User and Sys time statistics

Tweet Under Linux, the time command is quite convenient to get the elapsed time taken by a command call. It is very simple to use: just type your command preceded by the time command itself. For instance:

The output … Continue reading

Posted in Linux | 2 Comments

git : How to remove a big file wrongly committed

Tweet I added a large file to a git repository (102Mb), commited and push and got an error due to size limit limitations on github

Here, you see the path of the file (coverage/sensitivity/simualted.bed). So, the solution is actually … Continue reading

Posted in Computer Science | Tagged , | 2 Comments

git and github : skip password typing with https

Tweet If you clone a github repository using the https:// method (instead of ssh), you will have to type your username and passwor all the time. In order to avoid having to type you password all the time, you can … Continue reading

Posted in Computer Science | Tagged | Leave a comment