Author Archives: Thomas Cokelaer

No more space left on /tmp under Fedora

Tweet Under Fedora, one of my software requires more than 4Gb of temporary space and I realised that the /tmp directory is limited to 4Gb. In order to increase the /tmp directory, just edit the /etc/fstab file and add this … Continue reading

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blasr (pacbio) installation on fedora box

Tweet I wanted to use blasr tool for Pacbio mapping and had difficulties in using or installing the tool. I first use a local installation of the tool on the provided cluster and it look like the installation was quite … Continue reading

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swapping two columns with awk keeping tabulation

Tweet Assuming you have a data file with N columns and you want to swap the first and second one, just type:

To keep the tabulation intact, you need to specify the separator. Incoming separator is defined by -F … Continue reading

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set a default version to an environment module

Tweet Context: “The environment modules package provides for an easy dynamic modification of a user’s environment via modulefiles. which typically instruct the module command to alter or set shell environment variables such as PATH, MANPATH, etc. as well as define … Continue reading

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fedora aeroplane mode always on

Tweet Under Fedora 23, somehow the aeroplane mode went on (plane icon shown in top right corner). I tried to switch it off but could not. After a reboot, the aeroplane is still switch on and there is no way … Continue reading

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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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