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Monthly Archives: January 2018
git and github : skip password typing with https
if you clone a github repository using the https:// method (instead of ssh), you will have to type your username and passwor all the time. In order to avoid having to type you password all the time, you can use … Continue reading
failed to convert from cram to bam (parse error CIGAR character)
In order to convert a bioinformatic file from CRAM to BAM format, I naively used the samtools command available on a cluster but got this error: samtools view -T reference.fa -b -o output.bam input.cram [sam_header_read2] 3366 sequences loaded. [sam_read1] reference … Continue reading
How to mount and create a partition on a hard drive dock (fedora)
I got a new hard drive (2.7Tb) but wanted to use it with a docking station. Here are the steps required to use it under my Fedora box. First, I naively went into the Nautilus File Browser hoping to see … Continue reading
AWK: convert into lower or upper cases
In order to convert a bash variable to lower case with awk, just use this command: a="UPPER CASE" echo "$a" | awk ‘{print tolower($0)}’a="UPPER CASE" echo "$a" | awk ‘{print tolower($0)}’ If you want to convert the content of a … Continue reading
