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Top Forums Shell Programming and Scripting Command not found, but using function in bash Post 302962724 by cmccabe on Thursday 17th of December 2015 05:19:19 PM
Old 12-17-2015
Command not found, but using function in bash

In the bash below, if the answer is "y" then goto function remove. If the answer is "n" then goto the id variable line (where the date is inputted). However, I am getting command remove not found, but remove is a function not an command. I must have the syntax incorrect? Thank you Smilie.

Code:
#!/bin/bash
# README(v1) 12_16_2015

echo " Welcome to NGS module (v1) for medical exome analysis, the following steps will be performed
        ==================================
        1  remove @PG tag
        2  run picard markduplicates
        3  run picard HSmeterics
        4  run bedTools coverageBed
        5  detect bases less than 30 reads
        6  combine files
        =================================="
        
printf "\n\n"
printf "What is the date to analyze : "; read id
    date=$(date -d "$id" "+%m-%d-%Y") #convert to month-date-year
    [ -z "$id" ] && printf "\n No date supplied. Leaving match function." && sleep 2 && printf "\n Goodbye! " && exit
        for f in /home/cmccabe/Desktop/NGS/bam/$date/*.bam ; do
        bname=${f##*/}
        pref=${bname%%.bam}
        echo "detected ${pref}.bam in the directory"
done
printf "Are all the files there? "; read match_choice
case "$match_choice" in
        [yY]) remove ;;
        [nN]) printf "Not all the files are there, please find the missing files(s) and try again " && sleep 2 && printf "\n Goodbye! " && exit
        esac
remove() {
for f in /home/cmccabe/Desktop/NGS/bam/$date/*.bam ; do
    bname=`basename $f`
    pref=${bname%%.bam}
    samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > home/cmccabe/Desktop/NGS/bam/$date/${pref}_newheader.bam
done
}

 

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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)
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