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- Stan on python argparse issues with the help argument (TypeError: %o format: a number is required, not dict)
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- LP on AWK: the substr command to select a substring
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Author Archives: Thomas Cokelaer
Error while mounting external disk (NTFS is either inconsistent … $MFTMirr does not match $MFT)
I encountered a cryptic error message while trying to mount a disk under Fedora (39) using the desktop file manager. I went to the shell command to mount manually and hoping to get more information using sudo mount /dev/sda1 /run/media/cokelaer/ext … Continue reading
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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
