Forum:Looking for advice application devellopment

Question

[Titus]

Hi community :)

We project to develop an open source application to analyze bam file with different modules (variant calling, CHiP seq enrichment and other current NGS analysis). The main goal is to generate a database and give to the user a simple way to compare different sample result analyzed with the same parameters. So the user with a python interface will run easily NGS analysis with few enter files bam/cram and bed files.

First question: Is it to your opinion something which could be useful?

Second question: I'm not sure to know how to deal with software installation needed for the application (bwa, variant caller, samtools etc) to make it easy to install for the user. How to manage update of tool installation and right on the OS (linus of course :) )?. Do you have advice for this kind thinks?

Thanks in advance
Tristan

Answer 1

[Devon Ryan]

1. Yes that's useful, though keep in mind that there are a number of similar projects out there, none of which have become particularly popular. I think the reason behind this is that you end up needing to upload data to a remote server for comparisons, which most people don't want to do. Honestly, I'd try to tie something into MegaQC. Don't try to reinvent the wheel when it comes to doing QC, just come up with a convenient way to compare to other samples.
2. conda

[Titus]

Thank you Ryan. I didn't know about MegaQC i will check it :) Well our goal is to manage the analyze in local computer/server we do it in plus of out job no money for remote server :) But the popular question is complicate and our biggest fear. We hope to not reinvent the wheel but it's complicate to know what people needed plus than an other and to know that we need users ...

Answer 2

[Hussain Ather]

In response to your second question, definitely look at bioconda for installing packages.