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pachterlab / kallisto

Near-optimal RNA-Seq quantification
https://pachterlab.github.io/kallisto
BSD 2-Clause "Simplified" License
631 stars 168 forks source link

stdout result and platform independent #112

Open rhinempi opened 8 years ago

rhinempi commented 8 years ago

Hi, I am currently working on a cloud application using kallisto. The main issue are: 1, I am using cloud framework to mange fastq data distribution thus send and recieving data through stdin and stdout avoiding massive data IO. But, kallisto output a directory that can not by redirect to stdout. I modified the source code and changed the out put stream to stdout. But this brings the second question: 2, the compiled binary need a hdf5 library as a dependency, which is unsuitable for the concept of cloud as Platfor independent in multiple distributed computers.

I would be appreciated if someone could give me an idea or workaround.

Thanks!

Liren

rhinempi commented 8 years ago

Just finish benchmarking 3.1TB fastq.bz2 (~10TB raw) file to human transcript reference, decompressing plus kallistoing in 40mins. kallisto is faster than decompressing.