- This list will be updated gradually. See more intense bioinformatics one-liners at https://github.com/stephenturner/oneliners
Remove files from current folder based on the list in 'list.txt' using while loop. Replace rm with cp for copy to another folder!
while read -r f; do rm "$f"; done < list.txt
Submit many jobs at once to cluster (Hydra) from current folder based on file extension. Job files mafft.job, trimal.job and raxml.job required to be in the current directory, or give the PATH (e.g. /my/another/folder/mafft.job). -o is outout for the logs.
MAFFT:
for file in *.FNA; do qsub -o mafft-$file.log mafft.job $file; done
TrimAl:
for file in *.mafft; do qsub -o trimal-$file.log trimal.job $file; done
RAxML:
for file in *.fas; do qsub -o raxml-$file.log raxml.job $file; done
Send jobs based on the list in another file:
while read i; do qsub -o raxml-$i.log raxml.job $i; done < raxml-list.txt