Author Archives: Thomas Cokelaer

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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pypi upload failed due to non-existent authentication information

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

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

Great entry with description of RNA and DNA sequencing: enseqlopedia

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missing SAM header with minimap2 and samtools

When using minimap2 to map sequencing reads onto a reference, you can use this kind of command (be careful, this is wrong as you will see later): minimap2 -a -x map-pb test.fastq reference.fasta > minimap.samminimap2 -a -x map-pb test.fastq reference.fasta … Continue reading

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How to get pypi statistics about package download

A while ago, I designed pypiview, a Python package used to fetch the number of downloads for a package hosted on pypi website. It used to work decently but according to pypi itself the values stored are not reliable and … Continue reading

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How to prevent wget from creating duplicates

wget is used to download file from internet. For instance: wget http://url/test.csvwget http://url/test.csv So far so good but two things may happen. First, you may interrupt the download. Second, you may load the file again. Sometimes, files are huge and … Continue reading

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Meaning of Real, User and Sys time statistics

Under Linux, the time command is quite convenient to get the elapsed time taken by a command call. It is very simple to use: just type your command preceded by the time command itself. For instance: time dftime df The … Continue reading

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