The below code runs but no output is created. Thank you .
Code:
cmccabe@HPZ640:~/Desktop/NGS$ FILE=$(basename "$FILE")
cmccabe@HPZ640:~/Desktop/NGS$ for f
> do
> prefix=${f%%.bam}
> samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > /home/cmccabe/Desktop/NGS/pool_I_090215/${prefix}_newheader.bam
> done
tried this as well:
Code:
cmccabe@HPZ640:~/Desktop/NGS$ for f in /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/*.bam
> FILE=$(basename "$FILE")
bash: syntax error near unexpected token `FILE=$(basename "$FILE")'
cmccabe@HPZ640:~/Desktop/NGS$ do
bash: syntax error near unexpected token `do'
cmccabe@HPZ640:~/Desktop/NGS$ prefix=${f%%.bam}
cmccabe@HPZ640:~/Desktop/NGS$ samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > /home/cmccabe/Desktop/NGS/pool_I_090215/${prefix}_newheader.bam
bash: /home/cmccabe/Desktop/NGS/pool_I_090215//media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_016_150902_newheader.bam: No such file or directory
Last edited by cmccabe; 09-15-2015 at 06:15 PM..
Reason: added another code
How do I delete just the symbolic links in a directory? I have files that I wish to keep that have similar names, length and date/time. Can I use file size?
Thanks
kyle (4 Replies)
Hi All,
I was checking some of the files and I got the following entries:-
===============
v, 664, serv, serv, version.txt, exe
L, 775, serv, serv, start.sh, eventserv
================
Could someone please tell me what does the type"v" and "L" represent to.
I have not... (2 Replies)
hi
This should be easy but i'm obviously missing something obvious. :)
I'm looking to delete files from yesterday and older of extension .txt and there a range of subfolders with these files in them. The command runs but doesn't delete anything. SUSE 10.
find /testfolder -maxdepth 2 -type f... (6 Replies)
Can anyone see why the following command returns all files and not just the directories as specified?
find . -type d -exec ls -F {} \;
Also tried
find . -type d -name "*" -exec ls -F {} \;
find . -type d -name "*" -exec ls -F '{}' \; -print
Always returns all files :-\
OS is... (2 Replies)
Hi ! all
I have need of accessing multiple files of different type same base name, and I want to compare base name if matching then I want to send those 2 files of different type to some program, for further processing
my files are like this
file_1.txt
file_2.txt
file_3.txt
file_4.txt... (6 Replies)
hi,
I would like to delete files in a folder starting with letters ab and fe and so on. It should only delete if there are more than 3 files of that type in that folder. Please suggest me how to write a script. i am new to this scripting. (4 Replies)
I am not sure how to search and replace the word in the few specific files.
I need to search and replace word in only the name containing pepsi in the filename. (12 Replies)
find /tmp/testlog/kSR*"_"2018* -type f -printf '%T@ %p\n' | sort -n | tail -3 | cut -f2- -d" "
/tmp/testlog/log/KSR04_2018-07-05.log
/tmp/testlog/log/KSR04_2018-07-06.log
/tmp/testlog/log/KSR01_2018-07-06.log
But, I would see the following output(latest files for each KSR tuype)
... (3 Replies)
Discussion started by: jhonnyrip
3 Replies
LEARN ABOUT HPUX
dbs-edit-patch
DBS-EDIT-PATCH(1) Debian Build System DBS-EDIT-PATCH(1)NAME
dbs-edit-patch - Edit a DBS patch
SYNOPSIS
dbs-edit-patch [options] patch
dbs-edit-patch -h|--help
DESCRIPTION
dbs-edit-patch is script to generate or modify patches for Debian source-packages in DBS format.
WARNING
dbs is deprecated, please switch to the `3.0 (quilt)' Debian source package format instead. See http://wiki.debian.org/Projects/Deb-
Src3.0#FAQ for a short guide how to do it.
OPTIONS -h, --help
Show summary of options.
-t dir, --tmpdir=dir
Directory for the temporary files, default is /tmp or if set $TMP.
-s dir, --sourcedir=dir
Top level directory of the debian-package source-tree, default is the present working directory.
-P dir, --sourcepatchdir=dir
Directory containing upstream patches.
-T dir, --sourcetardir=dir
Directory containing the upstream tarball.
-p level, --strip=level
Striplevel -p of patch (Option -p of diff(1)), accepted values are 0 and 1, default is 0.
ENVIRONMENT VARIABLES
TMP Sets the directory for the temporary files, can be overridden with -t dir.
debian/vars
dbs-edit-patch will automatically use variables defined in the optional debian/vars file.
When a file debian/vars.in exists and debian/vars either does not exist or is older than any of the following files: debian/vars.in,
debian/changelog, debian/rules or debian/control, then dbs-edit-patch will try updating the vars file by running the following command
make -f debian/rules -W debian/vars.in debian/vars
EXAMPLES
Edit the 021_debian patch of Heimdal:
~/heimdal-0.3d> dbs-edit-patch -t/tmp 021_debian
Extracting source heimdal-0.3d.tar.gz ... successful.
Applying patch 001_replay ... successful.
etc.
Copying heimdal-0.3d to heimdal-0.3d-old ... successful.
Applying patch 021_debian ... successful.
Edit files under /tmp/021_debian/heimdal-0.3d as required, then put a short description into /tmp/021_debian/patch-description if desired,
and finally execute /tmp/021_debian/dbs-update-patch to save the results.
Technical note: dbs-edit-patch extracts all patches before 021_debian into /tmp/021_debian/heimdal-0.3d, copies the result to
/tmp/021_debian/heimdal-0.3d-old, and applies the last patch 021_debian (if it exists). Also, it creates a shell script which will create
the diff between the old and new directories:
~/heimdal-0.3d> ls -la /tmp/021_debian
total 12
-rwxr-xr-x 1 bam users 112 Jan 31 13:31 dbs-update-patch*
-rw-r--r-- 1 bam users 0 Jan 31 13:31 patch-description
drwxr-xr-x 14 bam users 4096 Jan 31 13:31 heimdal-0.3d/
drwxr-xr-x 14 bam users 4096 Jan 31 13:31 heimdal-0.3d-old/
drwxr-xr-x 5 bam users 4096 Jan 31 13:31 .stampdir/
~/heimdal-0.3d> cat /tmp/021_debian/dbs-update-patch
#!/bin/sh -e
cd "/tmp/021_debian"
HOOK_DIR="/usr/src/heimdal/debian/dbs-hooks"
test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-prediff
find -name "*.bak" -print0 | xargs -0 --no-run-if-empty rm
find -name "*~" -print0 | xargs -0 --no-run-if-empty rm
: > new_patch
test ! -e patch-description || cp patch-description new_patch
diff -ruN heimdal-0.3d-old heimdal-0.3d >> new_patch || test $? -eq 1
mv new_patch /usr/src/heimdal/debian/patches/021_debian
test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-postdiff
SEE ALSO diff(1), dbs(7), /usr/share/doc/dbs/
AUTHOR
DBS was written by Adam Heath, modified by Ben Collins, modified and packaged for Debian by Brian May. This manpage was generated by
Andreas Metzler and modified by Robert Luberda.
Debian February 15th, 2011 DBS-EDIT-PATCH(1)
09-15-2015
.