In the bash function below if the user selets "y" then the menu function is called and if they select "n" the move function is called. That all seems to work, my question is after the files are moved an echo,
line in bold is displayed and another function called backup is called. I am getting a syntax error on that line as that function, backup, can not be found. After the backup function executes another function run is called, hopefully. It seems very close but I'm not sure if I have the syntax for making the calls correct. Thank you .
Code:
additional() {
printf "\n\n"
printf "Are there additional files to be analyzed? Y/N "; read match_choice
case "$match_choice" in
[yY]) menu; break;;
[nN]) move; printf "Select folders are being copied to MedexPatients on medex as well as to the import folders "; break;;
esac
}
move() {
# move specific folders to MedexPatients on medex CIFS share
mkdir -p /home/cmccabe/medex/MedexPatients/$filename
rsync -av --exclude='/home/cmccabe/Desktop/NGS/API/$filename/bedtools' --exclude='/home/cmccabe/Desktop/NGS/API/$filename/torrent' --exclude='/home/cmccabe/Desktop/NGS/API/$filename/igv' /home/cmccabe/Desktop/NGS/API/$filename/bam /home/cmccabe/Desktop/NGS/API/$filename/fastqc /home/cmccabe/Desktop/NGS/API/$filename/lowcoverage /home/cmccabe/Desktop/NGS/API/$filename/panel /home/cmccabe/Desktop/NGS/API/$filename/picard /home/cmccabe/Desktop/NGS/API/$filename/vcf /home/cmccabe/Desktop/NGS/API/$filename/*.txt /home/cmccabe/Desktop/NGS/API/$filename/*.pdf /home/cmccabe/Desktop/NGS/API/$filename/*.log /home/cmccabe/medex/MedexPatients/$filename
# move to GenePerecent on CIFS share medex
rsync -av /home/cmccabe/Desktop/NGS/API/$filename/panel/20x/percent/*.txt /home/cmccabe/medex/GenePercent
# move to LowCoverage
rsync -av /home/cmccabe/Desktop/NGS/API/$filename/lowcoverage/20x/*.txt /home/cmccabe/medex/LowCoverage
# move to MedexVariants
rsync -av /home/cmccabe/Desktop/NGS/API/$filename/vcf/panel/annovar/*.txt /home/cmccabe/medex/MedexVariants
# move to Quality Metrics
rsync -av /home/cmccabe/Desktop/NGS/API/$filename/pdf/*.txt /home/cmccabe/medex/QualityMetrics
echo "analysis complete with new folder created and files moved to medex, the folder will now be sent to archive : $(backup)"
}
backup() {
# move folder to backup
printf "\n The directory will be moved to backup "; mv -v /home/cmccabe/Desktop/NGS/API/$filename /media/cmccabe/"My Book Western Digital"/ClinicalRuns; run ;;
}
Last edited by cmccabe; 03-28-2017 at 12:55 PM..
Reason: fixed format
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Discussion started by: ngabrani
2 Replies
LEARN ABOUT POSIX
libbash
LIBBASH(7) libbash Manual LIBBASH(7)NAME
libbash -- A bash shared libraries package.
DESCRIPTION
libbash is a package that enables bash dynamic-like shared libraries. Actually its a tool for managing bash scripts whose functions you may
want to load and use in scripts of your own.
It contains a 'dynamic loader' for the shared libraries ( ldbash(1)), a configuration tool (ldbashconfig(8)), and some libraries.
Using ldbash(1) you are able to load loadable bash libraries, such as getopts(1) and hashstash(1). A bash shared library that can be loaded
using
ldbash(1) must answer 4 requirments:
1. It must be installed in $LIBBASH_PREFIX/lib/bash (default is /usr/lib/bash).
2. It must contain a line that begins with '#EXPORT='. That line will contain (after the '=') a list of functions that the library
exports. I.e. all the function that will be usable after loading that library will be listed in that line.
3. It must contain a line that begins with '#REQUIRE='. That line will contain (after the '=') a list of bash libraries that are
required for our library. I.e. every bash library that is in use in our bash library must be listed there.
4. The library must be listed (For more information, see ldbashconfig(8)).
Basic guidelines for writing library of your own:
1. Be aware, that your library will be actually sourced. So, basically, it should contain (i.e define) only functions.
2. Try to declare all variables intended for internal use as local.
3. Global variables and functions that are intended for internal use (i.e are not defined in '#EXPORT=') should begin with:
__<library_name>_
For example, internal function myfoosort of hashstash library should be named as
__hashstash_myfoosort
This helps to avoid conflicts in global name space when using libraries that come from different vendors.
4. See html manual for full version of this guide.
AUTHORS
Hai Zaar <haizaar@haizaar.com>
Gil Ran <ril@ran4.net>
SEE ALSO ldbash(1), ldbashconfig(8), getopts(1), hashstash(1)colors(1)messages(1)urlcoding(1)locks(1)Linux Epoch Linux
03-28-2017
.