I have the following bash code. The for loop takes values from two successive locations of an array. Then it creates a corresponding directory in a cluster. There it creates a .cpki file and runs it in the cluster. Unfortunately this code stops working after first iteration.
declare -a CT
CT=(2 0 -1 -2)
len=${#CT[#]}
for ((i=0;i<len;i++)); do
a=${CT[$i]}
b=${CT[$((i+1))]}
input=${job_type}_${a}_${b}
WorkDir=/scratch/$USER/${input}.${JOB_ID} #Directory in a cluster
mkdir -p $WorkDir;
cd $WorkDir; #Go to cluster
...
Code that creates ${filename}.cpki file using a and b
...
$MPIRUN -np $NSLOTS $CP2K -i "${filename}.cpki"> "${filename}.cpko"
done
Please check whether len variable is changed unintentionally in the
Code that creates ${filename}.cpki file using a and b
part of the script.
Related
I am learning bash since 6 days I think I got some of the basics.
Anyway, for the wallpapers downloaded from Variety I've written two scripts. One of them moves downloaded photos older than 12 days to a folder and renames them all as "Aday 1,2,3..." and the other lets me select these and moves them to another folder and removes photos I didn't select. 1st script works just as I intended, my question is about the other
I think I should write the script down to better explain my problem
Script:
#!/bin/bash
#Move victors of 'Seçme-Eleme' to 'Kazananlar'
cd /home/eurydice/Bulunur\ Bir\ Şeyler/Dosyamsılar/Seçme-Eleme
echo "Select victors"
read vct
for i in $vct; do
mv -i "Aday $i.png" /home/eurydice/"Bulunur Bir Şeyler"/Dosyamsılar/Kazananlar/"Bahar $RANDOM.png" ;
mv -i "Aday $i.jpg" /home/eurydice/"Bulunur Bir Şeyler"/Dosyamsılar/Kazananlar/"Bahar $RANDOM.jpg" ;
done
#Now let's remove the rest
rm /home/eurydice/Bulunur\ Bir\ Şeyler/Dosyamsılar/Seçme-Eleme/*
In this script I originally intended to define another variable (let's call this "n") and so did I with copying and changing the variable from the first script. It was something like that
for i in $vct; do
n=1
mv "Aday $i.png" /home/eurydice/"Bulunur Bir Şeyler"/Dosyamsılar/Kazananlar/"Bahar $n.png" ;
mv "Aday $i.jpg" /home/eurydice/"Bulunur Bir Şeyler"/Dosyamsılar/Kazananlar/"Bahar $n.jpg" ;
n=$((n+1))
done
When I do that for the first time the script worked just as I intended. However, in my 2nd test run this script overwrote the files that already existed. I mean, for example in 1st run i had 5 files whose names are "Bahar 1,2,3,4,5" and the 2nd time I chose 3 files to add. I wanted their names to be "Bahar 6,7,8" but instead, my script made them the new 1,2 and 3. I tried many solutions and when I couldn't fix that I just assigned random numbers to them.
Is there a way to make this script work as I intended?
This command finds the biggest file name number amongst files in current directory. If no file is found, biggest number is assigned to 0.
biggest_number=$(ls -1 | sed -n 's/^[^0-9]*\([0-9]\+\)\(\.[a-zA-Z]\+\)\?$/\1/p' | sort -r -g | head -n 1)
[[ ! -z "$biggest_number" ]] || biggest_number=0
The regex in sed command assumes that there is no digit in filenames before the trailing number intended for increment.
As soon as you have found the biggest number, you can use it to start your loop to prevent overwrites.
n=$((biggest_number+1))
I made a shell script the purpose of which is to find files that don't contain a particular string, then display the first line that isn't empty or otherwise useless. My script works well in the console, but for some reason when I try to direct the output to a .txt file, it comes out empty.
Here's my script:
#!/bin/bash
# takes user input.
echo "Input substance:"
read substance
echo "Listing media without $substance:"
cd media
# finds names of files that don't feature the substance given, then puts them inside an array.
searchresult=($(grep -L "$substance" *))
# iterates the array and prints the first line of each - contains both the number and the medium name.
# however, some files start with "Microorganisms" and the actual number and name feature after several empty lines
# the script checks for that occurence - and prints the first line that doesnt match these criteria.
for i in "${searchresult[#]}"
do
grep -m 1 -v "Microorganisms\|^$" $i
done >> output.txt
I've tried moving the >>output.txt to right after the grep line inside the loop, tried switching >> to > and 2>&1, tried using tee. No go.
I'm honestly feeling utterly stuck as to what the issue could be. I'm sure there's something I'm missing, but I'm nowhere near good enough with this to notice. I would very much appreciate any help.
EDIT: Added files to better illustrate what I'm working with. Sample inputs I tried: Glucose, Yeast extract, Agar. Link to files [140kB] - the folder was unzipped beforehand.
The script was given full permissions to execute. I don't think the output is being rewritten because even if I don't iterate and just run a single line of the loop, the file is empty.
How do I rewrite the following to properly replace the variable with my genomeID? (I have it working with this method in Spades and Masurca assemblers, so it's something about Abyss that doesnt like this approach and I need a work-around)
I am trying to run abyss on a cluster server but am running into trouble with how abyss-pe is reading my variable input:
my submit file loads a script for each genome listed in a .txt file
my script writes in the genome name throughout the script
the abyss assembly fumbles the variable replacement
Input.sub:
queue genomeID from genomelisttest.txt
Input.sh:
#!/bin/bash
genomeID=$1
cp /mnt/gluster/harrow2/trim_output/${genomeID}_trim.tar.gz ./
tar -xzf ${genomeID}_trim.tar.gz
rm ${genomeID}_trim.tar.gz
for k in `seq 86 10 126`; do
mkdir k$k
abyss-pe -C k$k name=${genomeID} k=$k lib='pe1 pe2' pe1='../${genomeID}_trim/${genomeID}_L1_1.fq.gz ../${genomeID}_trim/${genomeID}_L1_2.fq.gz' pe2='../${genomeID}_trim/${genomeID}_L2_1.fq.gz ../${genomeID}_trim/${genomeID}_L2_2.fq.gz'
done
Error that I get:
`../enome_trim/enome_L1_1.fq.gz': No such file or directory
This is where "enome" is supposed to replace with a five digit genomeID, which happens properly in the earlier part of the script up to this point, where abyss comes in.
pe1='../'"$genomeID"'_trim/'"$genomeID"'_L1_1.fq.gz ...'
I added a single quote before and after the variable
I'm trying to run a shell script to get data from multiple directories.
My target (targetDir) has 5 directories. So the program, when executed, should search data from these 5 different directories, but when I execute it, it treats all the 5 folders same line. Any advice?
targetDir="snavis_bub snavis_bub2 snavis_bub3 snavis_hdw snavis_ldw"
datadir=/opt/pkg/home/tools/zform/marnel/$targetDir/of_inspect
Upon execute:
./orsInspect.sh: line 60:
cd: /opt/pkg/home/tools/zform/marnel/snavis_bub,snavis_bub2,snavis_bub3,snavis_hdw,snavis_ldw/oref_inspect: No such file or directory
Many things you can do. For example you can use arrays and for loops and perform a task each iteration of the loop:
#!/bin/bash
declare -a targetDirs=("snavis_bub" "snavis_bub2" "snavis_bub3" "snavis_hdw" "snavis_ldw")
for the_dir in "${targetDirs[#]}" ;do
datadir="/opt/pkg/home/tools/zform/marnel/${the_dir}/of_inspect"
echo "$datadir"
# ... do something for each datadir
done
example output (just echoing):
/opt/pkg/home/tools/zform/marnel/snavis_bub/of_inspect
/opt/pkg/home/tools/zform/marnel/snavis_bub2/of_inspect
/opt/pkg/home/tools/zform/marnel/snavis_bub3/of_inspect
/opt/pkg/home/tools/zform/marnel/snavis_hdw/of_inspect
/opt/pkg/home/tools/zform/marnel/snavis_ldw/of_inspect
I want to run a loop command on each pair of files
a_xxx.wig
b_xxx.wig
c_xxx.wig
a_xxx.bed
b_xxx.bed
c_xxx.bed
I'd like to match the files based on sample name (a,b or c) and have the loop run a command through each of the pairs without having to do one at a time
for file in * do
bedtools intersect -a $sample.wig -b $sample > $sample.bed
done
Any ideas or pointers would be greatly appreciated
The wig file is the input, so just iterate over those. You can extract the portion of the file name to use as the "base" for the other names.
for file in *.wig; do
sample=${file%.wig}
bedtools intersect -a "$sample.wig" -b "$sample" > "$sample.bed"
done