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|
Batch or not if/then
10-23-2014
. #!/bin/bash
while true
do
printf "Is this a batch : " ; read id
[ -z "$id" ] && break
If "$id" = Y, Then
[ "$id" = "end" ] && break
perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt
Else
If "$id" = N, Then
printf "Enter ID : " ; read id
[ -z "$id" ] && break
[ "$id" = "end" ] && break
perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo
done|
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DH-EXEC(1) dh-exec DH-EXEC(1) NAME
dh-exec - Debhelper executable file helpers SYNOPSIS
#! /usr/bin/dh-exec src/libfoo-*.so.* debian/foo-plugins/usr/lib/foo/${DEB_HOST_MULTIARCH}/ etc/example.conf => debian/foo/etc/foo/foo.conf DESCRIPTION
dh-exec is a simple program, meant to be used as the interpreter for executable debhelper config files. It is a wrapper around the various other sub-commands (see below), and will pipe the input file through all of them in turn, using an ordering that makes most sense in the vast majority of cases. The order as of now is dh-exec-subst gets run first, followed by dh-exec-install, so that variable expansion happens before files need to be copied. ARCHITECTURE
dh-exec is built up from three layers: there is the dh-exec utility, its single entry point, the only thing one will need to call. Below that, there are the various sub-commands, such as dh-exec-subst, dh-exec-installs and dh-exec-illiterate, which are thin wrappers around the various dh-exec scripts, that make sure they only run those that need to be run. And the lowest layer are the various scripts that do the actual work. One can control which sub-commands to run, or if even more granularity is desired, one can limit which scripts shall be run, too. See below for the options! OPTIONS
--with=command[,command ...] Replace the list of sub-commands to run the input through with a custom list (where entries are separated by whitespace or commas). This option will always replace the existing list with whatever is specified. This can be used to explicitly set which sub-commands to use. The list must not include the dh-exec- prefix. Defaults to subst,install. --without=command[,command ...] Inversely to the option above, this lists all the sub-commands which should not be used. The list must not include the dh-exec- prefix. --with-scripts=script[,script ...] Replace the list of scripts to run the input through with a custom list (where entries are separated by whitespace or commas). This option will always replace the existing list with whatever is specified. This can be used to explicitly specify which scripts to use, limiting even beyond what the --with option is capable of. The list must not include the dh-exec- prefix. By default it is empty, meaning there is no filtering done, and whatever scripts the sub-commands find, will be run. --no-act Do not really do anything, but print the pipeline that would have been run instead. --list List the available sub-commands and scripts, grouped by sub-command. --help, --version Display a short help or the package version, respectively. SUB-COMMANDS dh-exec-subst Substitutes various variables (either from the environment, or from dpkg-architecture(1)). dh-exec-install An extension to dh_install(1), that supports renaming files during the copy process, using a special syntax. ENVIRONMENT
DH_EXEC_LIBDIR The directory in which the wrapped sub-commands reside. Defaults to /usr/lib/dh-exec/. DH_EXEC_SCRIPTDIR The directory in which the scripts that do the heavy work live. Defaults to /usr/share/dh-exec/. FILES
$DH_EXEC_LIBDIR/dh-exec-* The various sub-commands. $DH_EXEC_SCRIPTDIR/dh-exec-* The various scripts ran by the sub-commands. SEE ALSO
debhelper(1), dh-exec-subst(1), dh-exec-install(1) AUTHOR
dh-exec is copyright (C) 2011-2012 by Gergely Nagy <algernon@madhouse-project.org>. 2012-05-03 DH-EXEC(1)