In the below code I am trying to combine two shell into one, but not sure if Im doing it right. Basically, there are 3 steps:
Step 1: the file conversion (which is underlined and asks the user if the file needs to be converted, if "y", then it runs the perl script if "n" then it skips to line 14
Code:
printf "Is this a batch or sanger analysis :" ; read id
)
Steps 2 and 3 already seem to work, but are asking the user if it is a batch or individual analysis, and if "y" one perl script is run, if "n" then another user prompt and perl command is run. Thanks .
Code:
#!/bin/bash
while true
do
printf "Does the file need to be converted : " ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
case "$id" in
[yY]) perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput
;;
[nN]) # code for X
Goto line 14
done
while true
do
printf "Is this a batch or sanger analysis :" ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
case "$id" in
[yY]) perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt
;;
[nN]) # code for X
printf "Enter ID : " ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
[ -z "$id" ] && break
[ "$id" = "end" ] && break
perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo
;;
end) break ;;
*) ;; # Unknown option, do nothing
esac
Goto line 4
done
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Hi All,
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cat /etc/shells
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Discussion started by: postcd
1 Replies
LEARN ABOUT SUNOS
chsh
CHSH(1) User Commands CHSH(1)NAME
chsh - change login shell
SYNOPSIS
chsh [options] [LOGIN]
DESCRIPTION
The chsh command changes the user login shell. This determines the name of the user's initial login command. A normal user may only change
the login shell for her own account; the superuser may change the login shell for any account.
OPTIONS
The options which apply to the chsh command are:
-h, --help
Display help message and exit.
-R, --root CHROOT_DIR
Apply changes in the CHROOT_DIR directory and use the configuration files from the CHROOT_DIR directory.
-s, --shell SHELL
The name of the user's new login shell. Setting this field to blank causes the system to select the default login shell.
If the -s option is not selected, chsh operates in an interactive fashion, prompting the user with the current login shell. Enter the new
value to change the shell, or leave the line blank to use the current one. The current shell is displayed between a pair of [ ] marks.
NOTE
The only restriction placed on the login shell is that the command name must be listed in /etc/shells, unless the invoker is the superuser,
and then any value may be added. An account with a restricted login shell may not change her login shell. For this reason, placing /bin/rsh
in /etc/shells is discouraged since accidentally changing to a restricted shell would prevent the user from ever changing her login shell
back to its original value.
FILES
/etc/passwd
User account information.
/etc/shells
List of valid login shells.
/etc/login.defs
Shadow password suite configuration.
SEE ALSO chfn(1), login.defs(5), passwd(5).
shadow-utils 4.5 01/25/2018 CHSH(1)
10-29-2014
.