Author Archives: Thomas Cokelaer

How to select genomic region using samtools

Posted on December 15, 2022 by Thomas Cokelaer

To select a genomic region using samtools, you can use the faidx command. This command is used to index a FASTA file and extract subsequences from it. Here is an example of how to use faidx to select a genomic … Continue reading →

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Nice vscode extensions

Posted on October 23, 2021 by Thomas Cokelaer

Whether you are a new developer, or an expert developer, you should really consider using vscode https://code.visualstudio.com I have to admit I have been using VIM for years and I believe  will always use it. I tried some great tools … Continue reading →

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

conda list command broken (unknown variable: python_implementation)

Posted on July 26, 2021 by Thomas Cokelaer

Recently I had my conda environment raising a long error report when calling conda list One of the relevant error message refers to an unknown variable python_implementation. raise SyntaxError(‘unknown variable: %s’ % expr) File “”, line None SyntaxError: unknown variable: … Continue reading →

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ipython autocompletion does not work

Posted on January 27, 2021 by Thomas Cokelaer

With IPython version 7.12.0 and python 3.7.3, Ipython crashes when I wanted to autocomplete a file or a module import. This fixed my problem: pip install pyreadline An the jedi package was set to 0.18.0 but this seems to cause … Continue reading →

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Setup ssh server on Fedora Linux platform

Posted on January 3, 2021 by Thomas Cokelaer

It could be useful to set up a SSH server on your Linux box. For instance, once set up, you can copy files from a Windows machine to your Linux box using ssh/ftp protocol. It is actually quite easy. Here, … Continue reading →

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How to use subprocess with PIPEs

Posted on November 16, 2020 by Thomas Cokelaer

In Python, the subprocess module allows you to execute linux/unix commands directly from Python. The official Python documentation is very useful would you need to go further. Yet it may be a bit scary for newbies. Syntax may also change … Continue reading →

Posted in Python | Tagged , | 1 Comment

Solved issue with the ultimate social media icons

Posted on June 1, 2020 by Thomas Cokelaer

In my wordpress blog, I suddenly got this error on every blog post: Notice: Undefined index: sfsi_original_counts in /var/www/wp-content/plugins/ultimate-social-media-icons/libs/controllers/sfsiocns_OnPosts.php on line 45 This was due to the ultimaqte-social-media plugin. Hopefully, it could be solved easily by going to the “Ultimate … Continue reading →

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Fedora 32 installation and post installation

Posted on May 31, 2020 by Thomas Cokelaer

A new laptop ! Great, let’s install a new Linux Fedora version. Insteresting to see that from 4 years ago, the version number has jumped from 23 to 32. 10 version in 4 years. Anyway. This is surely for the … Continue reading →

Posted in Linux | Tagged | 1 Comment

how to set the logging in DEBUG mode when using the python requests package

Posted on May 20, 2020 by Thomas Cokelaer

By default when using the excellent requests package, there is not much on the screen to figure out was goes wrong with a specific URL requests. In general, you do not need it but from time to time it is … Continue reading →

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sphinx raise a WARNING: Duplicate explicit target name:

Posted on April 24, 2020 by Thomas Cokelaer

Sphinx is a great tool for developers who want to write nice documentation about their software. I actually use it also to take notes or write about other stuff. From time to time I have a warning such as : … Continue reading →

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