I will give that a try. Alternatively since the results of the bash have the $filename value in it (in bold), maybe that could be extracted and stored as $filename.
log stored by the bash at /home/cmccabe/medex.logs/folder.log
Code:
The oldest folder is R_2017_01_13_12_11_56_user_S5-00580-24-Medexome, created on 2017-01-17+11:31:02.5035483130 and analysis done using v1.4 by cmccabe at 01/17/17 12:41:03 PM
So the R_2017_01_13_12_11_56_user_S5-00580-24-Medexome would be extracted and saved as $filename for the below processes to use.
Code:
(these are just two of 50 that all use the $filename variable)
I am going to repost as a new detail came up that I overlooked. Thanks again :).
mkdir -p /home/cmccabe/Desktop/NGS/API/$filename/{bam/{validation,coverage},bedtools,fastqc,hgmd,igv,panel/{reads,},panel/20x/{base,gene,percent},panel/{reads,},panel/30x/{base,gene,percent},pdf,picard,torrent,vcf/overall/{annovar,stats},vcf/panel/{annovar,}}
# create analysis log
echo "analysis done using v1.4 by $USER at $(date "+%D %r")" > /home/cmccabe/Desktop/NGS/API/$filename/analysis.txt
Thank you very much .
awk
Code:
awk -F" is " '{print $NF}' log
R_2017_01_13_12_11_56_user_S5-00580-24-Medexome, created on 2017-01-17+11:31:02.5035483130 and analysis done using v1.4 by cmccabe at 01/17/17 12:41:03 PM
Last edited by cmccabe; 01-17-2017 at 06:44 PM..
Reason: added not so perfect awk attempt
In a shell script, I am storing some values into variables. In between the code I am calling an PL/SQL precedure by connecting to ORACLE which generates a file. All this happens fine.
The problem is, the values are not getting stored in variables after this PL/SQL code while perfectly before... (1 Reply)
:)
Suppose,I have one table A. Table A have one column. Table A have 10 rows. I want this 10 rows store into shell script variable.
like
#!/bin/ksh
v_shell_var=Hi
here in call oracle , through loop How can I store table A's 10 rows into v_shell_var (Shell Script Array).
Regards,
Div (4 Replies)
Hi,
I'm trying to search a text file for a string: "energy(sigma->0)=". To do so, I executed the grep command, which returned many matches, for example:
energy without entropy = -112.16486170 energy(sigma->0) = -112.16520778
energy without entropy = -112.16488936 ... (5 Replies)
Hi,
I have few variable say 10
ex:-
l_pc_291334_01_0_01_00.cmp
l_pc_441133_50_0_02_00.cmp
l_pc_441133_55_0_02_00.cmp
Each variable value is coming via loop on a table.
I want to create a script that stores these value to a table or array ( But one by one not all at one time as... (4 Replies)
#!/bin/bash
#...
for i in `ls -c1 /usr/share/applications`
do
name="cat $i | grep ^Name= | cut -d = -f2"
echo $name
#...
done
Now inside name as output is present:
while i want only the result of the command.
Ideally i would like obtain that information using only bash ... or... (8 Replies)
My script gives the following result. Is it possible to display the same in table format ?
1.
rex_best
Latest feeds are not avaialable. The last feed was generated on 2012-05-17
File Name = ekb_best_20120517_010949_665.tar.gz
The Number of entry elements = 4209539
2.
rex_genre
Latest... (2 Replies)
In a directory i have a file *output* whose contents are changing for every simulation.
zgrep "trace file is" *output* | zgrep g
o/p: trace file is Int_01.1352176388z4f56ec33.0.trace.gz
I want to extract "Int_01.1352176388z4f56ec33.0.trace.gz" from the above result into a variable.
i... (2 Replies)
I'm attempting to write a bash script that will create a network between virtual machines. It accepts three arguments: an RSpec that describes the network topology, and two list of machines (servers and clients).
I have a (working) Perl script that I want to call. This Perl script takes an RSpec... (6 Replies)
The bash below loops through a specific directory dir and finds and writes the oldest folder to a variable called $filename.
#!/bin/bash
# oldest folder stored as variable for analysis, version log created, and quality indicators matched to run
dir=/home/cmccabe/Desktop/NGS/test
find... (2 Replies)
Discussion started by: cmccabe
2 Replies
LEARN ABOUT XFREE86
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
01-17-2017
.