Skip to content

Tag: linux

Alternative to cron that retains environment variables

I have been trying to set up a cron job to run a bash script every 30 minutes on a Linux-based compute cluster. The problem is that some functions normally available in my shell are not available to the cron job, causing it to crash. I import all my environment variables (including the ~/.bashrc) but no luck,…

How to iterate over two arguments in the sh linux shell

I have two sets of arguments: a = “5 7 1” and b = “dogs cats horse” They should come in pairs: 5 matches dogs, 7 matches cats and 1 matches horse They also should do this in one line: The problem is that the $a and $b can have hundreds of arguments, so writing many lines like the above

need perl to die when implicit open fails

I’m trying to migrate a sed script to a perl one-liner, because perl supports non-greedy regexp. I’ve taken advices from Non greedy (reluctant) regex matching in sed? and Why is my Perl in-place script exiting with a zero exit code even though it’s failing? I need my oneliner to exit with no…

Remove part of file name in multiple sub directories

The main folder “Main” contains multiple subfolders (6900,159, 9997, …) and each subfolder contains 8 items (4 files (6900Log.final.out, 6900Log.out, 6900Log.progress.out, 6900SJ.out.tab), 3 folders (6900_STARgenome, 6900_STARpass1, 6900_STARtmp), and one compressed file (6900Aligned.sortedB…

Renaming JSON files based on their contents

I have loads of geographical json files with date_geohash.json name format and I have to convert them to date_latitude-longotude.json format. For example I need to convert 2017-03-28_u13hhyn.json to 2017-03-28_N52.76-E1.62.json.   I’m trying to write a bash script to rename these json files using &#8216…