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Author Archives: Thomas Cokelaer
Efficient File Copying with Rsync: Including Only Certain File Types
When it comes to efficient and reliable file synchronization and copying, Rsync stands out as a powerful tool. Not only does it allow you to transfer files between local and remote locations, but it also offers the flexibility to include … Continue reading
How to select genomic region using samtools
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
Nice vscode extensions
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
conda list command broken (unknown variable: python_implementation)
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
ipython autocompletion does not work
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
Setup ssh server on Fedora Linux platform
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
How to use subprocess with PIPEs
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
Solved issue with the ultimate social media icons
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
Fedora 32 installation and post installation
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
how to set the logging in DEBUG mode when using the python requests package
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
