[Bioc-sig-seq] retrieving from SRA using fasp:

[ig2ar-saf2 at yahoo.co.uk]

Hello Vincent,

I tried to try the Aspera Firefox plug-in. I can describe the experience in a single word: obnoxious.

At the moment, it seems that command line guys like us will have to stick to good old ftp(*). To use your example, if you want 

fasp://
anonftp at ftp-private.ncbi.nlm.nih.gov:22/sra/static/SRX000/SRX000571/SRR002321.fastq.gz

you can get it like this

wget  wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/static/SRX000/SRX000571/SRR002321.fastq.gz

(*) this file is 2.7GB and it downloaded in ~4 minutes. You may call this bad old ftp depending on your expectations.

I hope somebody proves me wrong with Aspera.

Ivan



________________________________
From: Vincent Carey <stvjc at channing.harvard.edu>
To: bioc-sig-sequencing at stat.math.ethz.ch
Sent: Monday, 13 April, 2009 16:33:02
Subject: [Bioc-sig-seq] retrieving from SRA using fasp:

it seems that SRA is using the fasp: protocol to deliver data, at, say

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=faspftp_experiments&m=downloads&s=experiments

for example:

fasp://
anonftp at ftp-private.ncbi.nlm.nih.gov:22/sra/static/SRX000/SRX000571/SRR002321.fastq.gz

there is an aspera plugin for firefox that works, but it would be nice to
run from the command line.  there
seems to be something coming out of aspera, asperawebget, but it is not
clear how to obtain it.  i don't
want to request a trial version/be contacted by a salesperson.  anyone get
around this?

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