Reference Genome in snpEff Tool

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Reference Genome in snpEff Tool

Clint Christensen
Howdy!

I only see the "Caenorhabditis elegans: WS220.64" reference genome listed in the "Genome" drop down menu in the snpEff tool.  If possible, I would like to use the latest human genome hg19.  Can it be added as an option?  Thanks in advance.

Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy.

Clint Christensen
Research Assistant, Department of Genetics
Texas Biomedical Research Institute
7620 NW Loop 410
San Antonio, TX  78245
210-258-9779
[hidden email]



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Re: Reference Genome in snpEff Tool

Wang, Xiaofei
I have the same question. But, I want to use it on Drosophila and use SnpEff for CloudMap pipeline.
________________________________________
From: [hidden email] [[hidden email]] on behalf of Clint Christensen [[hidden email]]
Sent: Monday, February 17, 2014 10:01 AM
To: [hidden email]
Subject: [galaxy-dev] Reference Genome in snpEff Tool

Howdy!

I only see the "Caenorhabditis elegans: WS220.64" reference genome listed in the "Genome" drop down menu in the snpEff tool.  If possible, I would like to use the latest human genome hg19.  Can it be added as an option?  Thanks in advance.

Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy.

Clint Christensen
Research Assistant, Department of Genetics
Texas Biomedical Research Institute
7620 NW Loop 410
San Antonio, TX  78245
210-258-9779
[hidden email]



___________________________________________________________
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/



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Re: Reference Genome in snpEff Tool

Jennifer Jackson
Hi Clint, Xiaofei,

There are no current plans to include additional genomes to the SnpEff
tool on the public Main Galaxy instance at http://usegalaxy.org.

The best solution is to either run a local Galaxy (with sufficient
resources) or what is probably easier and more practical for many
scientific end users, a cloud Galaxy or possibly a Slipstream Appliance.
The tool wrapper is in the Tool Shed, so it can be installed and used
within your Galaxy, where you can add in any genome that you want that
has the appropriate reference data available.

Help to get started is in these links:
https://wiki.galaxyproject.org/BigPicture/Choices
https://wiki.galaxyproject.org/Tool%20Shed

Hopefully one of these solutions will work out for both of you!

Jen
Galaxy team

On 2/17/14 8:20 AM, Wang, Xiaofei wrote:

> I have the same question. But, I want to use it on Drosophila and use SnpEff for CloudMap pipeline.
> ________________________________________
> From: [hidden email] [[hidden email]] on behalf of Clint Christensen [[hidden email]]
> Sent: Monday, February 17, 2014 10:01 AM
> To: [hidden email]
> Subject: [galaxy-dev] Reference Genome in snpEff Tool
>
> Howdy!
>
> I only see the "Caenorhabditis elegans: WS220.64" reference genome listed in the "Genome" drop down menu in the snpEff tool.  If possible, I would like to use the latest human genome hg19.  Can it be added as an option?  Thanks in advance.
>
> Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy.
>
> Clint Christensen
> Research Assistant, Department of Genetics
> Texas Biomedical Research Institute
> 7620 NW Loop 410
> San Antonio, TX  78245
> 210-258-9779
> [hidden email]
>
>
>
> ___________________________________________________________
> 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/

--
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
Please keep all replies on the list by using "reply all"
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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
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Re: Reference Genome in snpEff Tool

Jennifer Jackson
Hi Xiaofei,

It is best to keep replied on the mailing list.

First, confirm that you are running the most current version of the
Galaxy distribution. This should be true by default if the installation
was just performed.
https://wiki.galaxyproject.org/DevNewsBriefs
https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10

Since you ran into this issue the first time the server was brought up
(or this appears to be the case), you may have run into a characterized
issue. On the http://getgalaxy.org page, are two work-arounds for
installing eggs in under specific usage circumstances. One is for when
running without internet access (probably not the issue). The other is
for when using Python 2.7 (my best guess as the problem). Both are
included about half-way down the wiki page, toward the end of the 'Start
it up' section:
https://wiki.galaxyproject.org/Admin/GetGalaxy

Please review and see if either if these apply, in particular if the
second command ("sh run.sh --reload") solves the issue.

Again, please keep feedback on the list, so that the developers can
assist us going forward as needed,

Jen
Galaxy team

On 2/24/14 9:51 AM, Wang, Xiaofei wrote:

> Dear Jen,
>
> I really appreciate for your reply!
>
> We decided to install the local Galaxy for this project. But, when I installed it (I followed the instruction on these 2 links, http://gmod.org/wiki/Galaxy_Tutorial_2013 and https://wiki.galaxyproject.org/Admin/GetGalaxy), I got a problem like this:
>
> $ sh run.sh
> Some eggs are out of date, attempting to fetch...
> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> Traceback (most recent call last):
>    File "./scripts/fetch_eggs.py", line 37, in <module>
>      c.resolve() # Only fetch eggs required by the config
>    File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve
>      egg.resolve()
>    File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve
>      return self.version_conflict( e.args[0], e.args[1] )
>    File "/Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict
>      r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch )
>    File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pkg_resources.py", line 576, in resolve
>      raise DistributionNotFound(req)
> pkg_resources.DistributionNotFound: pysam==0.4.2-kanwei-b10f6e722e9a
> Fetch failed.
>
> It seems a problem with the Python '"eggs". But, when I checked the version of Python, it is:
> $ python --version
> Python 2.7.6
>
> Could you help me about what is the problem with the installation?
>
> Thank you so much!
>
> Best,
>
> Xiaofei

___________________________________________________________
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Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org