[galaxy-user] Experience with Loading NGS data on standalone instance of galaxy

[Greg Von Kuster]

Ok, you have the change set.  Perhaps you are trying to upload into a 
history rather than a Data Library?  This new feature is only available 
for uploading into a Data Library.  Can you confirm?  I'm not sure what 
else could be causing you to not see the 4 options on the drop-down menu 
for uploading dataset into a Data Library.

Greg

Abhishek Pratap wrote:
> Here it is :
> 
>> hg heads
> 
> 
> changeset:   2824:d97f4e86be45
> tag:         tip
> parent:      2823:2c0c81150dbd
> parent:      2821:04a753865407
> user:        Anton Nekrutenko <anton at bx.psu.edu>
> date:        Fri Oct 02 11:02:14 2009 -0400
> summary:     merge
> 
> -Abhi
> 
> On Fri, Oct 2, 2009 at 3:30 PM, Greg Von Kuster <ghv2 at psu.edu> wrote:
>> Please type the following in your galaxy install directory, and let me know
>> what you get:
>>
>> hg heads
>>
>>
>> Thanks
>>
>> Abhishek Pratap wrote:
>>> Hi Greg
>>>
>>> Unfortunately it is not working for me. I made sure I cleared my
>>> browser cache before re-viewing it.
>>>
>>> I have set the option as suggested by you in the universe_wsgi.ini file.
>>>
>>> -Abhi
>>>
>>> On Fri, Oct 2, 2009 at 2:53 PM, Greg Von Kuster <ghv2 at psu.edu> wrote:
>>>> Hello Abhishek,
>>>>
>>>> Add this to your universe_wsgi.ini file:
>>>>
>>>> allow_library_path_paste = True
>>>>
>>>> Then, clicking the down-arrow on the upload form
>>>>
>>>> Create new data library datasets  ▼
>>>>
>>>> will give you 4 options, 1 of which is:
>>>>
>>>> Upload files from file system paths
>>>>
>>>> Greg Von Kuster
>>>> Galaxy Development Team
>>>>
>>>>
>>>> Abhishek Pratap wrote:
>>>>> Hi Greg
>>>>>
>>>>> I have updated my galaxy rep to changeset 2825. I dont see the
>>>>> checkbox on the "Upload File" page. Am I missing something ?
>>>>>
>>>>> Thanks,
>>>>> -Abhi
>>>>>
>>>>> On Fri, Oct 2, 2009 at 10:21 AM, Greg Von Kuster <ghv2 at psu.edu> wrote:
>>>>>> Change set 2812 will be included in a release to the distribution today
>>>>>> -
>>>>>> here are details of a new option that we're hoping will provide what is
>>>>>> needed for most labs.
>>>>>>
>>>>>> Add a new option, 'allow_library_path_paste' that adds a new upload
>>>>>> page
>>>>>> ("Upload files from file system paths") to the admin-side library
>>>>>> upload
>>>>>> pages.
>>>>>> This form contains a textarea that allows Galaxy admins to paste any
>>>>>> number
>>>>>> of
>>>>>> file system paths (files or directories) from which Galaxy will import
>>>>>> library
>>>>>> datasets, saving the directory structure (if desired).  Since such
>>>>>> ability
>>>>>> allows admins access to any file on the Galaxy server which is readable
>>>>>> by
>>>>>> Galaxy's system user, this option is disabled by default, and system
>>>>>> administrators should take care in assigning Galaxy administrators when
>>>>>> this
>>>>>> feature is enabled.  Controls on what files are accessible to this
>>>>>> tool
>>>>>> based
>>>>>> on ownership or other properties can be added at a later date if there
>>>>>> is
>>>>>> sufficient interest for such features.
>>>>>>
>>>>>> This commit also includes a checkbox on the "Upload directory of files"
>>>>>> page
>>>>>> (as well as the new "Upload files from file system paths" page above)
>>>>>> that
>>>>>> will
>>>>>> prevent Galaxy from copying data to its files directory (by default,
>>>>>> 'database/files/').  This is useful for large library datasets that
>>>>>> live
>>>>>> in
>>>>>> their own managed locations on the file system, this will prevent the
>>>>>> existence
>>>>>> of duplicate copies of datasets (but means administrators must take
>>>>>> care
>>>>>> to
>>>>>> manage data - moving or removing the data from its Galaxy-external
>>>>>> location
>>>>>> will render these datasets invalid within Galaxy).
>>>>>>
>>>>>> One unique feature to be aware of: when using the "Copy data into
>>>>>> Galaxy?"
>>>>>> checkbox on the "Upload directory of files" page, any symbolic links
>>>>>> encountered in the chosen import directory will be made absolute and
>>>>>> dereferenced ONCE.  This allows administrators to link large
>>>>>> datasets to
>>>>>> the
>>>>>> import directory, rather than having to make full copies, while being
>>>>>> able
>>>>>> to
>>>>>> delete such links after importing.  Only the first symlink (the one
>>>>>> in
>>>>>> the
>>>>>> import directory itself) is dereferenced; all others remain.  See
>>>>>> the
>>>>>> following
>>>>>> for an example:
>>>>>>
>>>>>> library_import_dir = /galaxy/import
>>>>>>
>>>>>> % ls -lR /galaxy/import
>>>>>> /galaxy/import:
>>>>>> total 6
>>>>>> drwxr-xr-x   2 nate     nate         512
>>>>>> Oct  1 11:31 link/
>>>>>>
>>>>>> /galaxy/import/link:
>>>>>> total 10
>>>>>> lrwxrwxrwx   1 nate     nate        
>>>>>>  71 Oct  1 10:38 1.bed ->
>>>>>> ../../../home/nate/galaxy/test-data/1.bed
>>>>>> lrwxrwxrwx   1 nate     nate        
>>>>>>  60 Oct  1 10:38 2.bed ->
>>>>>> /home/nate/galaxy/test-data/2.bed
>>>>>> lrwxrwxrwx   1 nate     nate        
>>>>>>  11 Oct  1 10:38 3.bed ->
>>>>>> ../../3.bed
>>>>>> lrwxrwxrwx   1 nate     nate        
>>>>>>  35 Oct  1 11:30 4.bed ->
>>>>>> ../../galaxy_symlink/test-data/4.bed
>>>>>> lrwxrwxrwx   1 nate     nate        
>>>>>>  41 Oct  1 11:31 5.bed ->
>>>>>> /galaxy/galaxy_symlink/test-data/5.bed
>>>>>>
>>>>>> % ls -l /galaxy/3.bed
>>>>>> lrwxrwxrwx   1 nate     nate        
>>>>>>  60 Oct  1 10:39
>>>>>> /galaxy/3.bed ->
>>>>>> /home/nate/galaxy/test-data/3.bed
>>>>>>
>>>>>> % ls -l /galaxy/galaxy_symlink
>>>>>> lrwxrwxrwx   1 nate     nate        
>>>>>>  44 Oct  1 11:30
>>>>>> /galaxy/galaxy_symlink
>>>>>> -> /home/nate/galaxy/
>>>>>>
>>>>>> In this example,
>>>>>>
>>>>>> 1.bed is a relative symbolic link to the real 1.bed.
>>>>>>
>>>>>> 2.bed is an absolute symlink to the real 2.bed.
>>>>>>
>>>>>> 3.bed is a relative symlink to ../../3.bed, aka /galaxy/3.bed, which
>>>>>> itself
>>>>>> is
>>>>>> a symlink to the real 3.bed.
>>>>>>
>>>>>> 4.bed is a relative symlink which follows another symlink
>>>>>> (/galaxy/galaxy_symlink) to the real 4.bed.
>>>>>>
>>>>>> 5.bed is an absolute symlink in the same fashion as 4.bed
>>>>>>
>>>>>> If the 'link' server directory is chosen on the "Upload directory of
>>>>>> files"
>>>>>> page, and "Copy data into Galaxy?" is checked "No", the following files
>>>>>> will
>>>>>> be
>>>>>> referenced by Galaxy:
>>>>>>
>>>>>> /home/nate/galaxy/test-data/1.bed
>>>>>> /home/nate/galaxy/test-data/2.bed
>>>>>> /galaxy/3.bed
>>>>>> /galaxy/galaxy_symlink/test-data/4.bed
>>>>>> /galaxy/galaxy_symlink/test-data/5.bed
>>>>>>
>>>>>> The Galaxy administrator may now safely delete /galaxy/import/link, but
>>>>>> should
>>>>>> take care not to remove the referenced symbolic links (/galaxy/3.bed,
>>>>>> /galaxy/galaxy_symlink).
>>>>>>
>>>>>> Not all symbolic links are dereferenced because it is assumed that if
>>>>>> an
>>>>>> administrator links to a path in the import directory which itself is
>>>>>> (or
>>>>>> contains) links, that is the preferred path for accessing the data.
>>>>>>
>>>>>>
>>>>>>
>>>>>> Oliver Hofmann wrote:
>>>>>>> Dear all,
>>>>>>>
>>>>>>>
>>>>>>> to echo what Abhi said: we are also currently looking of ways to
>>>>>>> automatically import data sets (libraries) into Galaxy without having
>>>>>>> to
>>>>>>> manually trigger the import via the administration interface, and
>>>>>>> ideally
>>>>>>> while keeping the data in the original place. The idea here is to have
>>>>>>> multiple tools all point at the original 'source data' without having
>>>>>>> to
>>>>>>> replicate terabytes of data.
>>>>>>>
>>>>>>> Not quite sure how feasible this is in practice, but it certainly
>>>>>>> would
>>>>>>> be
>>>>>>> incredibly helpful.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>>    Oliver
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 28 Sep 2009, at 14:24, Abhishek Pratap wrote:
>>>>>>>
>>>>>>>> HI Greg
>>>>>>>>
>>>>>>>> Thanks for a quick reply and making some requested changes. However I
>>>>>>>> am
>>>>>>>> not still sure if importing NGS data will help in long run.
>>>>>>>>
>>>>>>>> For Centers generating NGS data which could 2-3 T.B / week depending
>>>>>>>> on
>>>>>>>> no. of sequencers I think importing another copy of raw data into
>>>>>>>> galaxy
>>>>>>>> workspace will be asking for lot of disk space. I understand it is a
>>>>>>>> neat
>>>>>>>> way of doing things as it becomes agnostic of the raw data location
>>>>>>>>  but
>>>>>>>> might not be the best way for handling huge data in long run for
>>>>>>>> centers
>>>>>>>> like ours.
>>>>>>>>
>>>>>>>> Please correct me if I am wrong. I think we could also have a simple
>>>>>>>> option without having to import the data and just using it for
>>>>>>>> analysis
>>>>>>>> from
>>>>>>>> the current location, also storing results at the same location. That
>>>>>>>> way in
>>>>>>>> future even if the data set is moved analysis also stays with it.
>>>>>>>>
>>>>>>>> Let me know what you feel. I will be happy to know if there are any
>>>>>>>> other
>>>>>>>> smart reasons of importing the data in galaxy workspace just for
>>>>>>>> curiosity
>>>>>>>> sake.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> -Abhi
>>>>>>>>
>>>>>>>> On Mon, Sep 28, 2009 at 9:28 AM, Greg Von Kuster <ghv2 at psu.edu>
>>>>>>>> wrote:
>>>>>>>> Hello Abhishek,
>>>>>>>>
>>>>>>>> The Galaxy distribution includes the enhancements to which I
>>>>>>>> previously
>>>>>>>> referred for uploading history files.  Uploading files to a
>>>>>>>> history
>>>>>>>> now
>>>>>>>> creates a Galaxy job just like any other tool, and can be run on a
>>>>>>>> cluster
>>>>>>>> node, allowing upload of very large files.  The initial pass of
>>>>>>>> this
>>>>>>>> work is
>>>>>>>> also completed for uploading to a Data Library, but this enhancement
>>>>>>>> is
>>>>>>>> still in test, so it should soon be available in the distribution.
>>>>>>>>
>>>>>>>> Do you want to avoid having to import at all (e.g. allow Galaxy to
>>>>>>>> refer
>>>>>>>> to datasets that live in their original locations)?  This is not
>>>>>>>> currently
>>>>>>>> possible, but if this is what you are looking for, we can consider
>>>>>>>> some
>>>>>>>> additional options on the current upload form, or possibly a new,
>>>>>>>> separate
>>>>>>>> form.
>>>>>>>>
>>>>>>>>
>>>>>>>> Greg Von Kuster
>>>>>>>> Galaxy Development Team
>>>>>>>>
>>>>>>>>
>>>>>>>> Abhishek Pratap wrote:
>>>>>>>> Hi Greg, Anton and all
>>>>>>>>
>>>>>>>> Just wondering if there has been any progress made on this end. I am
>>>>>>>> sorry I was not able to follow it up on Assaf's suggestion due to
>>>>>>>> other
>>>>>>>> things at work.
>>>>>>>>
>>>>>>>> I did try the latest version of galaxy and looks like the files are
>>>>>>>> still
>>>>>>>> transferred over HTTP before they could be used in the galaxy
>>>>>>>> workspace.
>>>>>>>> Also I would again like to highlight that many labs might want to use
>>>>>>>> the
>>>>>>>> local instance of galaxy and prefer to point to a local path where
>>>>>>>> the
>>>>>>>> file
>>>>>>>> is being stored. That way we will have both the benefits of using a
>>>>>>>> cool GUI
>>>>>>>> and process data stored locally.
>>>>>>>>
>>>>>>>> Let me know if you guys need some feedback or have more questions. I
>>>>>>>> will
>>>>>>>> be happy to discuss them.
>>>>>>>>
>>>>>>>> best,
>>>>>>>> -Abhi
>>>>>>>>
>>>>>>>> On Tue, Jul 21, 2009 at 4:26 PM, Greg Von Kuster <ghv2 at psu.edu
>>>>>>>> <mailto:ghv2 at psu.edu>> wrote:
>>>>>>>>
>>>>>>>>   Hello Abishek,
>>>>>>>>
>>>>>>>>   We are currently in the process of significantly enhancing the
>>>>>>>>   current Galaxy upload utilities, and the new version should
>>>>>>>>   eliminate the issue you've raised about the time needed to
>>>>>>>> upload
>>>>>>>>   large files via HTTP ( not for making an initial copy of the
>>>>>>>> file in
>>>>>>>>   the Galaxy environment ). However, it will probably not be
>>>>>>>> ready for
>>>>>>>>   release for a few more weeks, so if you can take advantage of
>>>>>>>>   Assaf's script in the meantime, that's great. ¨ÜI can't
>>>>>>>> guarantee
>>>>>>>>   that all Galaxy features will function correctly if you do this
>>>>>>>> though.
>>>>>>>>
>>>>>>>>   Assaf, have you found that using your script breaks anything?
>>>>>>>>
>>>>>>>>   Also, if you upload a file to a library rather than a history,
>>>>>>>>   multiple users can "import" the library dataset into their
>>>>>>>> history
>>>>>>>>   for analysis, but there is only 1 file on disk ( users are
>>>>>>>> pointing
>>>>>>>>   to it from their histories ). ¨ÜBut uploading a file to
>>>>>>>> a history
>>>>>>>>   will create a new copy of the file each time it is uploaded.
>>>>>>>>
>>>>>>>>   Greg Von Kuster
>>>>>>>>   Galaxy Development Team
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>   Abhishek Pratap wrote:
>>>>>>>>
>>>>>>>>       Hi All
>>>>>>>>
>>>>>>>>       @Greg : Please find my comments below.
>>>>>>>>
>>>>>>>>       On Tue, Jul 21, 2009 at 10:44 AM, Greg Von
>>>>>>>> Kuster<ghv2 at psu.edu
>>>>>>>>       <mailto:ghv2 at psu.edu>> wrote:
>>>>>>>>
>>>>>>>>           Hello Abhi,
>>>>>>>>
>>>>>>>>           Can you clarify the steps you took that
>>>>>>>> produced the
>>>>>>>>           behavior? ǃÜSee my
>>>>>>>>
>>>>>>>>           comments below.
>>>>>>>>
>>>>>>>>           Anton Nekrutenko wrote:
>>>>>>>>
>>>>>>>>               Abhishek:
>>>>>>>>
>>>>>>>>               Let talk. This is the area
>>>>>>>> of active current
>>>>>>>>               development. We are
>>>>>>>> ǃÜlooking
>>>>>>>>
>>>>>>>>               at implementing a universal
>>>>>>>> fastq-like format or
>>>>>>>>               supporting
>>>>>>>> ǃÜmultiple
>>>>>>>>
>>>>>>>>               formats. Perhaps we should
>>>>>>>> join efforts in ironing
>>>>>>>> out
>>>>>>>>              
>>>>>>>> ǃÜspecifications.
>>>>>>>>
>>>>>>>>
>>>>>>>>               anton
>>>>>>>>               galaxy team
>>>>>>>>
>>>>>>>>
>>>>>>>>               On Jul 20, 2009, at 5:18
>>>>>>>> PM, Abhishek Pratap
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>                   Hi All
>>>>>>>>
>>>>>>>>
>>>>>>>>                   I recently came
>>>>>>>> to know about NGS analysis
>>>>>>>> on galaxy
>>>>>>>>                   during ISMB.
>>>>>>>>                   Getting excited
>>>>>>>> I tried couple of things
>>>>>>>> basically
>>>>>>>>                   to play with
>>>>>>>> it.
>>>>>>>>
>>>>>>>>                   Few comments :
>>>>>>>> I may have interepretted
>>>>>>>> something
>>>>>>>>                   described below
>>>>>>>> in a
>>>>>>>>                   wrong way. My
>>>>>>>> apologies before hand.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>                   On a standalone
>>>>>>>> installation of galaxy while
>>>>>>>> I was
>>>>>>>>                   trying to
>>>>>>>> explore
>>>>>>>>                   one
>>>>>>>> FASTQ(sequence) file. It takes
>>>>>>>> considerable (>
>>>>>>>>                   20 min) for a
>>>>>>>> fastq
>>>>>>>>                   file to get
>>>>>>>> uploaded (2 GB).
>>>>>>>>
>>>>>>>>           Are you using the Galaxy upload utility
>>>>>>>> to create an
>>>>>>>> item in
>>>>>>>>           your history
>>>>>>>>           that points to the dataset file on
>>>>>>>> disk?
>>>>>>>>
>>>>>>>>
>>>>>>>>       Yes that is precisely correct, I am trying to
>>>>>>>> upload a solexa
>>>>>>>> FASTQ
>>>>>>>>       file but on a standalone galaxy installation from
>>>>>>>> my local
>>>>>>>> file
>>>>>>>>       system.
>>>>>>>>
>>>>>>>>           I am not sure what is the rationale
>>>>>>>>
>>>>>>>>                   behind that.
>>>>>>>> Ideally I think there should be
>>>>>>>> no need
>>>>>>>>                   to upload such
>>>>>>>>                   heavy files
>>>>>>>> into the workspace.
>>>>>>>>
>>>>>>>>           A data file that originates from a
>>>>>>>> place external to
>>>>>>>> Galaxy
>>>>>>>>           must be uploaded
>>>>>>>>           into Galaxy so that the disk file can
>>>>>>>> be placed in the
>>>>>>>>           location configured
>>>>>>>>           in the Galaxy config file.
>>>>>>>> ǃÜAlso, when data is
>>>>>>>> uploaded to
>>>>>>>>
>>>>>>>>           Galaxy ( either
>>>>>>>>           to a history or a library ), several
>>>>>>>> database table
>>>>>>>> settings
>>>>>>>>           are created
>>>>>>>>           that are used by various Galaxy
>>>>>>>> features.
>>>>>>>>
>>>>>>>>           They could actually be used straight
>>>>>>>>
>>>>>>>>
>>>>>>>>       Thanks for the clarification but I am not sure this
>>>>>>>> will help
>>>>>>>> a
>>>>>>>>       lot of
>>>>>>>>       people who are interested to install and run galaxy
>>>>>>>> locally
>>>>>>>>       mainly for
>>>>>>>>       the following reasons. May be it is just local to
>>>>>>>> me.
>>>>>>>>
>>>>>>>>       A. We already one instance of data saved on the
>>>>>>>> local file
>>>>>>>> system
>>>>>>>>       B. Making another copy via galaxy will eat away a
>>>>>>>> lot of space
>>>>>>>>       in long run.
>>>>>>>>       C. The time needed to import the files into galaxy
>>>>>>>> space is
>>>>>>>> huge
>>>>>>>>
>>>>>>>>                   away by the
>>>>>>>> path specified.
>>>>>>>>
>>>>>>>>           What do you mean by "the path
>>>>>>>> specified"?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>       Well what I mean was a way to specify the path of
>>>>>>>> the file/run
>>>>>>>>       on the
>>>>>>>>       lcoal file system and galaxy could directly pick it
>>>>>>>> up from
>>>>>>>> there
>>>>>>>>       rather than uploading it into its own space. Now I
>>>>>>>> understand
>>>>>>>> this
>>>>>>>>       might not work based on the way the system was
>>>>>>>> designed.
>>>>>>>>
>>>>>>>>
>>>>>>>>           Also is there any way to access the
>>>>>>>>
>>>>>>>>                   scripts for
>>>>>>>> analysis on the command line. I
>>>>>>>> know
>>>>>>>>                   this undermines
>>>>>>>> the
>>>>>>>>                   main aim of
>>>>>>>> working with galaxy but rite now
>>>>>>>> I am
>>>>>>>>                   concerned about
>>>>>>>> the
>>>>>>>>                  
>>>>>>>> performance/time.
>>>>>>>>
>>>>>>>>           You should be able to run any Galaxy
>>>>>>>> tool from the
>>>>>>>> command
>>>>>>>>           line as long as
>>>>>>>>           you have all of the tool's required
>>>>>>>> binaries in your
>>>>>>>> path.
>>>>>>>>           ǃÜHowever, running
>>>>>>>>
>>>>>>>>           a tool from within Galaxy should
>>>>>>>> generally not be any
>>>>>>>> slower
>>>>>>>>           than running it
>>>>>>>>           outside of Galaxy, depending, of
>>>>>>>> course, on what you are
>>>>>>>> doing.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>       Ok I was under the impression that running from
>>>>>>>> SHELL will
>>>>>>>> eliminate
>>>>>>>>       the step of uploading them into galaxy file space.
>>>>>>>>
>>>>>>>>
>>>>>>>>       -Abhi
>>>>>>>>
>>>>>>>>                   I will be happy
>>>>>>>> to discuss more about this
>>>>>>>> in case
>>>>>>>>                   you have some
>>>>>>>>                  
>>>>>>>> comments/questions for me.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>                   Best,
>>>>>>>>                   -Abhi
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>                  
>>>>>>>> -----------------------------
>>>>>>>>
>>>>>>>>                   Abhishek Pratap
>>>>>>>>
>>>>>>>>                   Bioinformatics
>>>>>>>> Software Engineer
>>>>>>>>
>>>>>>>>                   Institute for
>>>>>>>> Genome Sciences
>>>>>>>>
>>>>>>>>                   School of
>>>>>>>> Medicine, Univ of Maryland
>>>>>>>>
>>>>>>>>                   801, W.
>>>>>>>> Baltimore Street, Baltimore, MD
>>>>>>>> 21209
>>>>>>>>
>>>>>>>>                   Ph:
>>>>>>>> (+1)-410-706-2296
>>>>>>>>
>>>>>>>>                  
>>>>>>>> www.igs.umaryland.edu/
>>>>>>>> <http://www.igs.umaryland.edu/>
>>>>>>>>                  
>>>>>>>> _______________________________________________
>>>>>>>>                   galaxy-user
>>>>>>>> mailing list
>>>>>>>>                  
>>>>>>>> galaxy-user at bx.psu.edu
>>>>>>>> <mailto:galaxy-user at bx.psu.edu>
>>>>>>>>
>>>>>>>>
>>>>>>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>>>>>>>>
>>>>>>>>               Anton Nekrutenko
>>>>>>>>               http://nekrut.bx.psu.edu
>>>>>>>>               http://galaxyproject.org
>>>>>>>>
>>>>>>>>              
>>>>>>>> _______________________________________________
>>>>>>>>               galaxy-user mailing list
>>>>>>>>               galaxy-user at bx.psu.edu
>>>>>>>> <mailto:galaxy-user at bx.psu.edu>
>>>>>>>>
>>>>>>>>              
>>>>>>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> galaxy-user mailing list
>>>>>>>> galaxy-user at bx.psu.edu
>>>>>>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>>>>>>> --
>>>>>>> Research Associate    Department of Biostatistics
>>>>>>> Associate Director    Bioinformatics Core
>>>>>>>                    
>>>>>>>  Harvard School of Public Health
>>>>>>> Skype: ohofmann       Phone: +1 (617) 365 0984
>>>>>>>
>>>>>>>
>>>>>>>
>>