1. Further Command line… Nic Bertrand CEH IT Support, GRID & Bioinformatics

2. Content Compression, archiving utilities Input/Output/Error redirection Pipes Who is using that file? (lsof, fuser)

3. Compression/Uncompression Linux supports the compression of a wide range of archiving formats:.zip,.tar,.gz,.Z,.bz2

4. Tar Most common use: Uncompress an archive: Tar xvf archive.tar Tar xvzf archive.tar.gz Tar xvjf archive.tar.bz2 Check an archive: Tar tf archive.tar Tar tzf archive.tar.gz

5. tar -- tape Archiving Utility Creating an archive: Tar cvf archive.tar *.txt Built-in gzip/bzp2 function: tar cvzf archive.tar.gz *.txt tar cvjf archive.tar.bz2 *.txt

6. Gotchas with tar… never use absolute paths when creating an archive... e.g. don’t do: tar cvf home_archive.tar /home Check the content of a tar file using tar tf

7. Moving file tree using tar –cd /sourcedir tar cf -. | (cd /destdir && tar xpf -)

8. gzip Compressing: gzip file -> file.gz.gz is compressed Uncompressing: gzip -d file.gz or gunzip file.gz

9. Other compression formats Software Common extension compress/uncompress.Z zip/unzip.zip bzip2/bunzip2.bz2 Warnings: Linux does not support windows self-extractable.exe zip archives Bio-Linux does not support ARJ archives “out of the box”

10. Checking file types: file Used to determine the file type examples: binary, ASCII text, GNU tar format… Examples: feeding an binary ‘text’ file (word document) into clustalw or blastall will not work…

11. Input/output redirection write standard output to file Myprog > output.txt Append standard output to file Myprog >> output.txt Standard error to standard output Myprog >outputfile 2>&1

12. More I/O redirection Normal mode: –myprog > output.txt (send stdout to file) –myprog 2> error.txt (send stderr to file) –myprog > allout.txt 2>&1 (send stdout and stderr to file) –myprog < inputfile (take stdin from file) –myprog 2> /dev/null (chuck stderr into oblivion!) Append: –myprog >> output.txt (send stdout to end of file) –myprog 2>> error.log (send stderr to end of file) –myprog >> allout 2>&1 (send stdout and stderr to end of file) –myprog <<x (take stdin until "x" occurs) Pipes: myprog | myprog2 (pipe stdout of myprog to stdin of myprog2) myprog 2>&1 | myprog2 (pipe stdout and stderr of myprog to myprog2)

13. Getting info on what/who is using a file/device/socket Crucial info if: You want to unmount device, partition and and you get a frustrating ‘umount: device is busy’ LSOF and FUSER are useful tools

14. lsof: list open files lsof /mnt/cdrom what/who is using the cdrom? lsof –i :505 what is using TCP port 505?

15. fuser: identify processes using files or sockets man fuser list all process accessing port: fuser ssh/tcp fuser -mk /home/user1 lists all processes using /home/user1 and terminates them!

16. Exercises 1. list processes that access the /var partition 2. list processes that use the ssh port a. using fuser b. using lsof3. 3. Launch Artemis. Consult the man page for fuser and figure out a way to send a kill signal to all process that use /usr/software What happens? 4. list all manual pages relevant to password 5. email the man passwd page to your email account 6. cd ~manager/examples/further_cli/tar/Compress all the blast reports (.blastp) files into a tar.gz file 7. cd../compressedexpand compressed.tar file in current directory 8. Compress/gzip all.prot files. What sort of compression ratio do you get? Can you alter/improve this?