Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
20
gravatar for Phil Ewels
9 months ago by
Phil Ewels470
Sweden / Stockholm / SciLifeLab
Phil Ewels470 wrote:

Hi all,

As a fun little side project I've made a web tool to find runs on the NCBI Sequence Read Archive (SRA) and fetch the download URLs for these. You can do all of this in a couple of clicks, hopefully quite a bit easier than navigating the main SRA pages.

In addition to getting the SRA links the tool now queries the European Nucleotide Archive (ENA) for direct FastQ downloads and also provides these URLs.

All links are given as a simple list and also as a bash script which uses curl to download the data and gives nicer filenames that include the sample name in addition to its accession number.

You can find the tool here: https://ewels.github.io/sra-explorer/

It's open source and in fact just a single HTML file, built using AngularJS and Bootstrap. If you're curious, you can find the code here: https://github.com/ewels/sra-explorer

Phil

ADD COMMENTlink modified 7 weeks ago by psschlogl20 • written 9 months ago by Phil Ewels470
2

Shopping basket/add files you need to collection

sra4

URLs

sra1

bash script

sra2

If you prefer .sra downloads

sra3

ADD REPLYlink modified 9 months ago • written 9 months ago by genomax75k
2

Amazing! Works like a charm! Thanks so much!

ADD REPLYlink written 9 months ago by jean.elbers1.3k

Works great, very useful utility, thank you!

ADD REPLYlink written 3 months ago by hermidalc0
1

Very convenient, thank you, also for multiqc! You might consider adding an option to provide links for downloads driven by Aspera as in my tutorial Fast download of FASTQ files from the European Nucleotide Archive (ENA). That speeds up downloads notably.

ADD REPLYlink modified 9 months ago • written 9 months ago by ATpoint26k
1

Nice idea and great tutorial! I've just added this functionality - it would be great if you could have a look and make sure that I haven't made any errors.. Note that I added an option to append a mv command to rename the files. I've never used Aspera myself, so I hope this actually works!

ADD REPLYlink written 9 months ago by Phil Ewels470
1

Cool, works fine!

ADD REPLYlink modified 9 months ago • written 9 months ago by ATpoint26k

Nice tool...i used and works fine......👍🙏

ADD REPLYlink written 7 weeks ago by psschlogl20

Hi Phil Ewels, could you please modify the download paths one gets when clicking the Aspera commands for downloading FastQ files button for OSX. Currently it is

$HOME/Applications/Aspera\ Connect.app/Contents/Resources/asperaweb_id_dsa.openssh

but should be Aspera_Connect.app so the whitespace in the folder name be replaced with underscore. Otherwise that whitespace causes error when running the command. Only saw that issue recently as I never download on Mac but only Linux. As one needs to manually rename the Aspera folder on the Mac machine for this to work, maybe a pop-up would be good when choosing OSX that either tells the user to rename that folder manually or a link to the tutorial ( Fast download of FASTQ files from the European Nucleotide Archive (ENA) ) telling that one should check it out for details on how to make it work for Mac.

Thanks!

ADD REPLYlink modified 17 days ago • written 17 days ago by ATpoint26k

Hi ATpoint,

I'm a little confused - doesn't the backslash in the command escape the whitespace? Usually paths with two\ words are fine (two words would not be). What error do you see? In the post reporting this problem I can only see paths without the backslash escape, so I can understand why that was a problem.

Example of different behaviours:

$ mkdir "folder with space"
$ cd folder\ with\ space/
$ pwd
/Users/ewels/folder with space
$ cd ../
$ cd "folder with space"
$ pwd
/Users/ewels/folder with space
$ cd ../
$ cd folder with space
-bash: cd: folder: No such file or directory

Phil

ADD REPLYlink written 17 days ago by Phil Ewels470

You're right. The thing is that the awk command removed the actual escape character so instead of

$HOME/Applications/Aspera\ Connect.app/Contents/Resources/asperaweb_id_dsa.openssh

it is

$HOME/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.openssh

I think simply changing this part of the awk command into

$HOME/Applications/Aspera\\ Connect.app/ instead of $HOME/Applications/Aspera\ Connect.app/ should do it. Stupid mistake from my side, sorry.

ADD REPLYlink modified 17 days ago • written 17 days ago by ATpoint26k

Ok great! Glad you got it sorted. No problem at all :)

ADD REPLYlink written 14 days ago by Phil Ewels470
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