Author Archives: Thomas Cokelaer

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

Posted in Software development | Tagged | Leave a comment

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

Posted in Linux | Tagged | Leave a comment

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

Posted in wordpress | Leave a comment

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

Posted in Linux | Tagged | Leave a comment

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

Posted in Linux | Tagged | Leave a comment

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

Posted in Uncategorized | Tagged | Leave a comment

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

Posted in Linux | Tagged , | Leave a comment

All about RNA and DNA sequencing

Great entry with description of RNA and DNA sequencing: enseqlopedia

Posted in bioinformatics | Tagged , , | Leave a comment

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

Posted in bioinformatics | Tagged , | Leave a comment

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

Posted in Python | Tagged , , , | Leave a comment