I have a set of bioinformatics tools. Now I want to execute them one by one in a automated sequence where data (output ) generated by one tool will be used as an input in the next tool.
I am new to programming and bioinformatics so if you can give me the codes to implement such a automated execution string I will be grateful.
The tools are such.
1. BWA-mem 2. SAM to BAM converter 3. BAM to VCF converter 4. ClinEff/ SNP Eff/ or VEP 5. Meta SVM 6. Genome Browser 7. KEGG
You can put all the commands you want to run in order on the linux shell separated with a semicolon symbol (;), be careful to put the same names if outputs in the inputs of the next step.
The other option that I know is to write every command in a Ruby script between ` symbol, like this: `blastn -query .... `. You can put each command in a new line, always between the ` symbol and the run the script.
Good look!!!
Dear Saikat,
For this purpose I can recommend bpipe that is nicely described here (http://bpipe-test-documentation.readthedocs.io/en/latest/Overview/Introduction/). Besides allowing to define pipelines it writes log files (so you exactly know what it was doing) and allows to resume the pipeline at a specific stage.
If you would be spending a long time in Bioinformatics, learn shell script as there is no escape from programming! You can somehow manage to do the stuff by asking questions and getting ready-made answers but there will be times when you will be looking at others to help you. So, why not start googling like this (it works, believe me!): how to run samtools from bash /shell script for -------- and so on. Later, how to pipe commands in shell? So and so forth. You will realize that this will help you in a long run. Cheers!!
thanks for all your answers but what i am actually looking for is automation. i have tried to build a docker container and call the tools one by one though a ruby script but the code still has quite a number of bugs. Is there any method to apply machine learning to achieve the automation?
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