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2d
comment Help in starting learning bash script
The backslashes are used in a case like this for escaping newline characters. Thus, telling the shell interpreter to read the lines ending in \ as a single long line. Having the backslashes in between arguments in the shell doesn't really matter, as you're only escaping the space character following them. It just makes it harder to read.
2d
comment Help in starting learning bash script
Yes. That's pretty much it. afile="/some/path/to/A.IndelRealigner.intervals". Then in both commands, substitute that variable. First command: -o $afile. Second command: -targetIntervals $afile. Then do the same with the other variables that are used twice.
Nov
24
comment Help in starting learning bash script
And why do you have all the extra "\" backslash characters?
Nov
24
comment Help in starting learning bash script
A bash script like the one you have above is a procedural script. That is, the first command runs, and when it is finished, the second command runs. There is no explicit passing of data from the first to the second, other than what is written to files by the first, and read from the same files by the second. Depending on what output you need passed to the first one, there are a number of ways to do that, such as capturing output in a variable in the script, and using that variable in subsequent commands, or using pipes (cmd1 | cmd2) where STDOUT of cmd1 is passed to STDIN of cmd2
Nov
24
answered Help in starting learning bash script
Oct
29
awarded  Good Answer
Oct
4
awarded  Custodian
Aug
6
reviewed Approve suggested edit on How to uncompress zlib data in UNIX?
Aug
6
reviewed Approve suggested edit on spice tag wiki
Aug
6
reviewed Approve suggested edit on What is the long ID that Linux assigns to a disk in /media/?
Aug
6
comment Debugging a Solaris network issue
Those port 53 queries you see in netstat -an are just your fileserver trying to do DNS lookups.
Jul
20
reviewed Approve suggested edit on Spoofing or removing DHCP client hostname in response to DHCP server
Jul
13
awarded  Nice Answer
Jul
2
awarded  Good Answer
Jun
20
comment Script runs manually but not from cron
Sorry. I meant to say a reduced environment. Cron often doesn't run script with the same environment a user would get in an interactive shell.
Jun
19
comment Script runs manually but not from cron
Thanks, @l0b0 . I guess it just looks funny to me. :)
Jun
19
answered Script runs manually but not from cron
Jun
19
reviewed Approve suggested edit on Script runs manually but not from cron
Jun
16
comment Disallow Changing of Passwords
good suggestion! using a VM in this way would provide a good learning environment.
Jun
16
comment Where should I place my websites files with multiple vhosts?
While the answers are correct that it doesn't really matter where you put them, I would offer that /var/www/site1, /var/www/site2 is a widely used convention that will be familiar to many folks, so standardizing there can be beneficial.