Ah. The file stout.miRNA.bash.$date_formatted is capturing the stdout from all three programs. I am trying to extract lines from the Cutadapt stdout and the sRNAbench stdout here. The fastQC is writing the summary.txt.
Quote:
"$LOCATION"/Sample_* matches all sample files (not folders).
This is actually a folder (containing the actual data being processed).
Quote:
What exactly do these paths / filenames have in common? You can't use * to match one and * to match the other when you want pairs, since they both expand to complete lists. Do you find the sample in Sample_abcde, and the summary in abcde_fastqc ?
The Location is the Project (a folder with many sample data folders); The Sample_* is the data folder for each sample; the *_fastqc is the output folder for each sample from one program, fastqc, where each folder contains a summary.txt.
thank you for taking the time. I really appreciate your help.
In bash, I need to send the STDOUT and STDERR from a command to one file, and then just STDERR to another file. Doing one or the other using redirects is easy, but trying to do both at once is a bit tricky. Anyone have any ideas? (9 Replies)
Is there a way to redirect all stdout to a file implicitly - like defining stdout=/home/me/process.log - so that all "echo" commands in several scripts/subscripts are written to that file; instead of having to edit all scripts to redirect the "echo" (e.g. echo 'This is a test ' >>... (1 Reply)
Hi,
I am trying to execute a command like this:
find ./ -name "*.gz" -exec sh -c 'zcat {} | awk -f parse.awk' \; >> output
If I want to print the filename, i generally use the -print argument to the find command but when I am redirecting the output to a file, how can I print just the... (2 Replies)
I have an executable that, depending on its input, outputs to either one file or several. It usually prints nothing on screen. The usual way to call this program is to specify an input and output filenames, like this:
./executable.exe -i inputfile -o outputfileIt will then try to use the output... (1 Reply)
can anyone help me in making singleline command for
Capital Letters are folders ,small letter are files
X,Y,Z are subfolders of A
as shown below
A - X,Y,Z
Folder X has three files a.txt,b.txt,c.txt similarly Y,Z.
as shown below
X- a.txt,b.txt,c.txt
Y- a.txt,b.txt,c.txt
Z-... (4 Replies)
Hi everybody,
I am trying to do the thing you see in the title, and I can't simply do
a=$(svn up)
echo $a
because the program (svn) gives output on lots of lines and in the variable the output is stored on only one line (resulting in a horribly formatted text). Any tips?
Thanks,... (2 Replies)
Hello,
I have a script (videostream.sh) which invokes the GStreamer command-line tool gst-launch with all the correct command line parameters. When I invoke this program, I add the '&' character at the end to make it a background task, so that my script can complete and exit, i.e.
gst-launch... (1 Reply)
I have a simple bash script that prints sth every 5 seconds. What I do is the following. I redirect the output of the script to a file, tail the file and see that it works and then from another console I delete the file where the output is redirected to. Even though I have deleted the file, the... (2 Replies)
I have a C program that continously outputs info to stdout. The problem is that I am redirecting the stdout and stderr to a file and stdout is written at the end of the problem rather than continously to the file. This could be a problem if for example the program is killed and the stdout output is... (3 Replies)
Hello,
I'm strugling with some redirecting and all help is apreciated.
The following program is working as expected, but the result of the AT command doesn't go to any file.
Thanks in advance for the help.
#!/bin/bash
modem=/dev/ttyUSB1
file=/root/imsi.txt
# print error to stderr and exit... (4 Replies)
Discussion started by: cleitao
4 Replies
LEARN ABOUT OSX
new
NEW(1) [nmh-1.5] NEW(1)NAME
new - report on folders with new messages
fnext - set current folder to next folder with new messages
fprev - set current folder to previous folder with new messages
unseen - scan new messages in all folders with new messages
SYNOPSIS
new [sequences] [-mode mode] [-folders foldersfile] [-version] [-help]
fnext is equivalent to new -mode fnext
fprev is equivalent to new -mode fprev
unseen is equivalent to new -mode unseen
DESCRIPTION
New in its default mode produces a one-line-per-folder listing of all folders containing messages in the listed sequences or in the
sequences listed in the profile entry "Unseen-Sequence". Each line contains the folder, the number of messages in the desired sequences,
and the message lists from the .mh_sequences file. For example:
foo 11.* 40-50
bar 380. 760-772 824-828
total 391.
The `*' on foo indicates that it is the current folder. The last line shows the total number of messages in the desired sequences.
New crawls the folder hierarchy recursively to find all folders, and prints them in lexicographic order. Override this behavior by provid-
ing foldersfile containing the pre-sorted list of folders new should check, one per line.
In fnext and fprev modes, new instead changes to the next or previous matching folder, respectively.
In unseen mode, new executes scan sequences for each matching folder.
FILES
$HOME/.mh_profile The user profile
PROFILE COMPONENTS
Path: To determine the user's nmh directory
Current-Folder: To find the default current folder
Unseen-Sequence: The name of the unseen message sequence
SEE ALSO scan(1), mh-format(5)HISTORY
Based on Luke Mewburn's new (http://www.mewburn.net/luke/src/new).
MH.6.8 11 June 2012 NEW(1)