Author Archives: Thomas Cokelaer

packet_write_wait: Connection to XXX : Broken pipe

Tweet In general, I can connect to a remote machine via SSH without any troubles but occasionally in some particular setup, although I can connect to the remote machine and type commands in a shell, the connection is broken after … Continue reading

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pytest-cov collects no data on Travis

Tweet I recently switched from nosetests to pytest and pytest-cov for one of my Python project ( Locally, everything seemed to work fine and once on Travis, all tests passed as expected. Yet, before the coverage report, I noticed this … Continue reading

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Remove extension in a bash script

Tweet Imagine a bunch of files with extension fastq.dsrc, the following script will decompress the files by looping over the N files. One issue was to remove the extension in the script. See below the usage of //

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git synchronisation of a forked repository

Tweet Let us assume you have forked a repository (from You now have a local version at a given time of the repository repository_name.

Time flyes and you come back to the local repository and you are not … Continue reading

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gimp: how to make a transparent background

Tweet How to make a transparent background/selection on an image using GIMP 1. Open your image. 2. Select the area you want to make transparent. Select the appropriate selection tool from the Tool window or the Tools – Selection Tools … Continue reading

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lost your linux root password ?

Tweet Lost your root password ? ========================= Under Fedora, at boot time, press e, select the kernel and add 1 (run level), which will let you enter into a shell session, where you can edit the /etc/passwd file to reset … Continue reading

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vim: multiple buffers

Tweet In order to work with several view ports of the same file in the same Vim window, type:

You may also open another file in the same window. To do so issue the command::

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vim: create function to remove white spaces

Tweet In the .vimrc file, add the following lines ( here ^M is a special character for the return carriage created using CTRL+V):

those functions call then be called within vim typing:

some Explanation of the function removeWhiteSpace(). … Continue reading

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yumex-dnf is locked

Tweet Under Fedora 23, starting yumex-dnf, I got a message that yumex-dnf was locked. I could not find any lock file in /var/cache/dnf and therefore was stuck. Finally, running

did kill the faulty process and could start yumex-dnf again…

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conda and bioconda channel

Tweet Anaconda ( ) provides a Python distribution with more than 400 of the most popular Python packages for science, math, engineering, and data analysis. Anaconda installs an executable called conda that will be your entry point. Anaconda solves … Continue reading

Posted in biology, Python | Tagged , , | 1 Comment