Author Archives: Thomas Cokelaer

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

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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

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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

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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

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sphinx raise a WARNING: Duplicate explicit target name:

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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bioconda (how to build recipe locally)

Bioconda is great. From their web site, “it is a channel for the conda package manager specializing in bioinformatics software”. It provides over 7000 bioinformatics packages ready to use with conda install and over 850 contributors and 570 members who … Continue reading

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How to Mount and Use an exFAT Drive on Fedora Linux

Yesterday, I got this hard drive from a collaborator with huge amount of sequencing data on it. Under fedora 23, I pluged in the hardrive, open the browser, click on the hard drive name and and got this error message: … Continue reading

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Updated wordpress version crashed the wp-admin access

From the wordpress admin interface, I updated the plugins and the wordpress to 5.2.2 but ot this unplesant error: Parse error: syntax error, unexpected ‘[‘ in /home/xxxx/www/blog/wp-content/plugins/googleanalytics/class/Ga_Admin.php on line 375Parse error: syntax error, unexpected ‘[‘ in /home/xxxx/www/blog/wp-content/plugins/googleanalytics/class/Ga_Admin.php on line 375 … Continue reading

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git error solved: The remote end hung up unexpectedly

Sometimes, when you clone a git repository you may end up with a fatal error “The remote end hung up unexpectedly”. For instance, typing this git command to clone a repository of mine: git clone https://github.com/sequana/sequanagit clone https://github.com/sequana/sequana led to … Continue reading

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How to find differences between two directories using diff command

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 checking … Continue reading

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