Creating steps in bash script - bash

Question

To start, I am relatively new to shell scripting. I was wondering if anyone could help me create "steps" within a bash script. For example, I'd like to run one analysis and then have the script proceed to the next analysis with the output files generated in the first analysis.
So for example, the script below will generate output file "filt_C2":
./sortmerna --ref ./rRNA_databases/silva-arc-23s-id98.fasta,./index/silva-arc-23s-id98.db:./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-id98.db:./rRNA_databases/silva-euk-18s-id95.fasta,./index/silva-euk-18s-id95.db:./rRNA_databases/silva-euk-28s-id98.fasta,./index/silva-euk-28s-id98.db:./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-database-id98.db:./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s.db --reads ~/path/to/file/C2.fastq --aligned ~/path/to/file/rrna_C2 --num_alignments 1 --other **~/path/to/file/filt_C2** --fastx --log -a 8 -m 64000
Once this step is complete, I would like to run another step that will use the output file "filt_C2" that was generated. I have been creating multiple bash scripts for each step; however, it would be more efficient if I could do each step in one bash file. So, is there a way to make a script that will complete Step 1, then move to Step 2 using the files generated in step 1? Any tips would be greatly appreciated. Thank you!

Answer 1

Welcome to bash scripting!
Here are a few tips:
You can have multiple lines, as many as you like, in a bash script file.
You may call other bash scripts (or any other executable programs) from within your shell script, just as Frank has mentioned in his answer.
You may use variables to make your script more generic, say, if you want to name your result "C3" instead of "C2". (Not shown below)
You may use bash functions if your script becomes more complicated, e.g. see https://ryanstutorials.net/bash-scripting-tutorial/bash-functions.php
I recommend placing sortmerna in a directory that is in your environmental PATH variable, and to replace the multiple ~/path/to/file to another variable (say WORKDIR) for consistency and flexibility.
For example, let’s say you name your script print_analysis.sh:
#!/bin/bash
# print_analysis.sh
# Written by Nikki E. Andrzejczyk, November 2018
# Set variables
WORKDIR=~/path/to/file
# Stage 1: Generate filt_C2 using SortMeRNA
./sortmerna --ref ./rRNA_databases/silva-arc-23s-id98.fasta,./index/silva-arc-23s-id98.db:./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-id98.db:./rRNA_databases/silva-euk-18s-id95.fasta,./index/silva-euk-18s-id95.db:./rRNA_databases/silva-euk-28s-id98.fasta,./index/silva-euk-28s-id98.db:./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-database-id98.db:./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s.db \
--reads "$WORKDIR/C2.fastq" \
--aligned "$WORKDIR/rrna_C2" \
--num_alignments 1 \
--other "$WORKDIR/filt_C2" \
--fastx --log -a 8 -m 64000
# Stage 2: Process filt_C2 to generate result_C2
./stage2 "$WORKDIR/filt_C2" > "$WORKDIR/result_C2.txt"
# Stage 3: Print the result in result_C2
less "$WORKDIR/result_C2.txt"
Note how I use trailing backslash \ so that I could split the long sortmerna command into multiple shorter lines, and the use of # for human-readable comments.
There is still room for improvement as mentioned above but not implemented in this quick example, but hope this quick example shows you how to expand your bash script and make it do multiple steps in one go.
Bash is actually a very powerful scripting and programming language. To learn more, you may want to start with Bash tutorials like the following:
https://ryanstutorials.net/bash-scripting-tutorial/
http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html
Hope this helps! If you have any other questions, or if I had misunderstood your question, please feel free to ask!
Cheers,
Anthony