I am trying to select a file in bash and save it to a directory. The below does run but no selected file is saved. Thank you .
bash
Code:
# select file
printf "please select a file to analyze with entered gene or genes \n"
select file in $(cd /home/cmccabe/Desktop/NGS/API/test/bedtools;ls);do break;done
echo $file "will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for vizulization, and calculate 20x and 30x coverage for the entered gene(s)"
logfile=/home/cmccabe/Desktop/NGS/API/test/process.log
for file in /home/cmccabe/Desktop/NGS/API/test/bedtools/$file; do
echo "Start selcted file creation: Panel: ${FUNCNAME[0]} Date: $(date) - File: $file"
bname=$(basename $file)
pref=${bname%%.txt}
while read -r file; do mv "$file" /home/cmccabe/Desktop/NGS/panels/reads/${pref}_OTHER.txt ; done
echo "End selected file creation: $(date) - File: $file"
done >> "$logfile"
Hi,
I'm trying to write a function that redirects the contents of an
array to a file. The array contains the lines of a data file with
white space.
The function seems to preserve all white space when redirected
except that it seems to ignore newlines. As a consequence, the
elements of the... (7 Replies)
Hi
I need to execute a select statement in a solaris environment with oracle database. The select statement returns number of rows of data.
I need the data to be inserted into a CSV file with proper format. For that we normally use "You have to select all your columns as one big string,... (2 Replies)
Hi there.
i have created a program that in the end it will give output like this
1 2 3 4 5
10 9 8 7 6
11 12 13 14 15
.............. 17
i wonder how to save the output into a single string and into a file.
i.e 1 10 11 12 9 2 3 8 13 14 7 4 5 6 15 17 (in this order,... (3 Replies)
Use and complete the template provided. The entire template must be completed. If you don't, your post may be deleted!
1. The problem statement, all variables and given/known data:
Hi there.
i have created a program that in the end it will give output like this
1 2 3 4 5
10 9 ... (1 Reply)
I am using bash to prompt a user for a choice using: where a "y" response opens a menu with available panels that can be used.
while true; do
read -p "Do you want to get coverage of a specific panel?" yn
case $yn in
* ) menu; break;;
* ) exit;;
* ) echo... (6 Replies)
The `bash` below uses the oldest folder in the specified directory and logs it. The goes though an analysis process and creates a log. My problem is that if there are 3 folders in the directory folder1,folder2,folder3, the bash is using folder2 for the analysis eventhough folder1 is the oldest... (0 Replies)
In the bash below I am asking the user for a panel and reading that into bed. Then asking the user for a file and reading that into file1.Is the grep in bold the correct way to apply the selected panel to the file? I am getting a syntax error. Thank you :)
... (4 Replies)
In the bash below the oldest folder in a directory is selected. If there are 3folders in the directory /home/cmccabe/Desktop/NGS/test and nothing is done to them (ie. no files deleted, renamed) then the bash correctly identifies f1 as the oldest. However, if something is done to the folder then... (4 Replies)
#!/bin/bash
X=(2H 4S 10D QC JD 9H 8S)
How do I unset the 10D from this array and save it to a file?
Please use CODE tags as required by forum rules! (5 Replies)
Discussion started by: cogiz
5 Replies
LEARN ABOUT DEBIAN
rbash
RBASH(1) General Commands Manual RBASH(1)NAME
rbash - restricted bash, see bash(1)RESTRICTED SHELL
If bash is started with the name rbash, or the -r option is supplied at invocation, the shell becomes restricted. A restricted shell is
used to set up an environment more controlled than the standard shell. It behaves identically to bash with the exception that the follow-
ing are disallowed or not performed:
o changing directories with cd
o setting or unsetting the values of SHELL, PATH, ENV, or BASH_ENV
o specifying command names containing /
o specifying a file name containing a / as an argument to the . builtin command
o specifying a filename containing a slash as an argument to the -p option to the hash builtin command
o importing function definitions from the shell environment at startup
o parsing the value of SHELLOPTS from the shell environment at startup
o redirecting output using the >, >|, <>, >&, &>, and >> redirection operators
o using the exec builtin command to replace the shell with another command
o adding or deleting builtin commands with the -f and -d options to the enable builtin command
o using the enable builtin command to enable disabled shell builtins
o specifying the -p option to the command builtin command
o turning off restricted mode with set +r or set +o restricted.
These restrictions are enforced after any startup files are read.
When a command that is found to be a shell script is executed, rbash turns off any restrictions in the shell spawned to execute the script.
SEE ALSO bash(1)GNU Bash-4.0 2004 Apr 20 RBASH(1)
06-18-2016
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