Re: [galaxy-user] Fwd: Converting files to gd_snp format

[Cathy Riemer]

Hello Mike,

The tutorial you were looking at was made using one of our local Galaxy
instances, in advance of updating the main public server.  The main server
already includes most of the tools used in the examples, but two of the
format conversion tools (MasterVar to gd_snp and pgSnp to gd_snp) are
not posted there yet.

I apologize for the delay.  We are in the process of moving some of the tools
from the Phenotype Association section of the toolbox to the Convert Formats
section, while simultaneously migrating those and the rest of the Phenotype
Association tools from their current, manually configured installation method
to the new Galaxy Tool Shed paradigm.  We have encountered some technical
difficulties with that, but we hope to have the update accomplished within
the next few weeks.

If you need it sooner, let me know and I'll send you the underlying Perl
script for the pgSnp to gd_snp tool, so you can run that locally to
convert your file and then upload the output to your Galaxy history.

Thanks for your patience!

-Cathy Riemer


  -- Forwarded message --
  From: Sheehan, Michael - (michaelsheehan) michaelshee...@email.arizona.edu
  Date: Wed, Jan 30, 2013 at 1:30 AM
  Subject: [galaxy-user] Converting files to gd_snp format
  To: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu
 

  I would like to convert VCF files to gd_snp format to be used in some
  population genomic analyses. A tutorial online makes it seem like this
  is the correct path to follow to conduct such analyses:

  http://www.bx.psu.edu/~giardine/tutorials/example2/part1/snpTable.html

  I have been using Galaxy on the free public server and this tools does
  not appear to be present anywhere. Does anyone know where the tool has
  gone or is there a way to add the needed tools back?

  Thanks
  Mike

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[galaxy-user] Fwd: Question about FTP

[Cathy Riemer]

- Forwarded message from Noushin Ghaffari noushin.ghaff...@gmail.com -

Date: Mon, 7 Mar 2011 09:09:13 -0600
From: Noushin Ghaffari noushin.ghaff...@gmail.com
To: dbad...@bio.cse.psu.edu
Subject: Question about FTP

Dear Galaxy team,

Firstly, thank you very much for the great tools.

I am working on a large dataset and need to upload it to Galaxy via FTP. I
used

ftp://main.g2.bx.psu.edu

but I cannot login. I used my email, my public name on Galaxy and just
simple my name, but none of them worked. Can you please help me to know how
can I login to upload my file?

Here is my inofrmation:

email: noushin.ghaff...@gmail.com

public name: me-on-galaxy

I appreciate you help and time in advance.

Noushin

- End forwarded message -
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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use the Galaxy Development list:

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