Download histories

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Download histories

Doan, Ryan

Hello,

 

Several people in our lab would like to download all of their histories from their respective Galaxy accounts. We tried to download them using the following steps:

 

Select “Export to File”

 

Copy the provided link and paste into WGet.exe program as follows:

 

wget.exe --no-check-certificate https://main.g2.bx.psu.edu/history/export_archive?id=e0b0f57abd62f2aa -O F:\Galaxy\Ryan\rnd003bucknell.edu\Cattle_seq.galaxy

 

However, we seem to be getting an error on all files from all of their accounts and no files are being saved. See below for cmd prompt output.

 

Resolving main.g2.bx.psu.edu... 128.118.250.4

Connecting to main.g2.bx.psu.edu|128.118.250.4|:443... connected.

WARNING: cannot verify main.g2.bx.psu.edu's certificate, issued by `/C=US/O=Inte

rnet2/OU=InCommon/CN=InCommon Server CA':

  Self-signed certificate encountered.

WARNING: certificate common name `bigsky.bx.psu.edu' doesn't match requested hos

t name `main.g2.bx.psu.edu'.

HTTP request sent, awaiting response... 200 OK

Length: unspecified [text/html]

Saving to: `C:/Users/RDoan/Documents/Lab_Files/Analysis_Programs/Galaxy/test.txt

 

 

 

Is this the correct method to download histories or is there a better solution?

 

Thank you for your help!

Ryan

 

 


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Re: Download histories

Jeremy Goecks
You'll need to wait until the history is ready for download -- i.e., Galaxy provides a .gz file rather than a Webpage at that URL -- before using wget. Galaxy returns a webpage (text/html) while preparing the history for download; this is likely what you are downloading now.

Good luck,
J.



On Jun 13, 2013, at 4:16 PM, Doan, Ryan wrote:

Hello,
 
Several people in our lab would like to download all of their histories from their respective Galaxy accounts. We tried to download them using the following steps:
 
Select “Export to File”
 
Copy the provided link and paste into WGet.exe program as follows:
 
wget.exe --no-check-certificate https://main.g2.bx.psu.edu/history/export_archive?id=e0b0f57abd62f2aa -O F:\Galaxy\Ryan\rnd003bucknell.edu\Cattle_seq.galaxy
 
However, we seem to be getting an error on all files from all of their accounts and no files are being saved. See below for cmd prompt output.
 
Resolving main.g2.bx.psu.edu... 128.118.250.4
Connecting to main.g2.bx.psu.edu|128.118.250.4|:443... connected.
WARNING: cannot verify main.g2.bx.psu.edu's certificate, issued by `/C=US/O=Inte
rnet2/OU=InCommon/CN=InCommon Server CA':
  Self-signed certificate encountered.
WARNING: certificate common name `bigsky.bx.psu.edu' doesn't match requested hos
t name `main.g2.bx.psu.edu'.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/html]
Saving to: `C:/Users/RDoan/Documents/Lab_Files/Analysis_Programs/Galaxy/test.txt
 
 
 
Is this the correct method to download histories or is there a better solution?
 
Thank you for your help!
Ryan
 
 
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/