Author Archives: Thomas Cokelaer

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


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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:


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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)


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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


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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


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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


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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


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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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pypi upload failed due to non-existent authentication information


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After trying to upload a package on Pypi website using python setup.py sdist upload I got this error message: Submitting dist/XXX-0.7.5.tar.gz to https://upload.pypi.org/legacy/ Upload failed (403): Invalid or non-existent authentication information. error: Upload failed (403): Invalid or non-existent authentication information.Submitting … Continue reading

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format USB key under fedora


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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: This partition cannot be modified … Continue reading

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All about RNA and DNA sequencing


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Great entry with description of RNA and DNA sequencing: enseqlopedia

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