I have been trying to run this command (that I have run before in a different directory), and everything I've read on the message boards has not solved my unknown issue.
Of note: 1) the files exist in this directory 2) I have proper permissions to move these files around 3) I have run this exact line of code before and it has worked. 4) I tried listing files with and without '' to capture all the files (see below). 5) I also tired to list each file as 'Sample1', but that did not work.
xargs -a [filename.txt] mv -t [new-directory]
I have file beginnings (I have ~5 file for each beginning), and I want to move all the files associated with that beginning.
Example: Sample1.bam Sample1.sorted.bam, etc The lines in the file are listed as such: Sample1* Sample2* Sample3* ...etc.
What am I doing incorrectly and how can I fix it? TIA!
When you execute command using 'xargs' arguments are passed directly to the called program ('mv' in your case). Wildcard patterns in the input are not expanded - 'sample1*' is passed as is to "mv", which issue an error message about note having a file named 'sample1*'.
To get file name expansion, you want to use the shell. One way to handle this situation is
xargs -a FILENAME.TXT -I__ sh -c "mv -t NEW-FOLDER -- __"
Security Note: the code provides some protection against command line injection (e.g., file name starting with '-'). However, other possible attacks are possible. Safer version is
cat FILENAME.txt | grep '^[A-Za-z0-9][A-Z-z0-9._-]*$' | xargs I__ sh -c "mv -t NEW-FOLDER -- __"
which will limit the input to file with alphanumeric. The 'grep' patterns can be extend the pattern as needed.