[galaxy-dev] Re: [galaxy-bugs] Job running problems

[Jennifer Hillman-Jackson]

Hi David,

If you are running the work at a public Galaxy server, the queue times
for larger compute-intensive tools are usually a bit longer than for
simpler tools.

The best strategy is to queue jobs up and allow those to fully process. If
you delete and rerun, that will place the new job back at the end of the
queue again, further extending wait time. The only reason to rerun is if
you already know there is a problem with the inputs that will likely lead
to a job failure (or results you don't want).

For urgent or time-sensitive work, or if you'd just like to have more quota
space and not compete with others for common public resources, consider
setting up your own Galaxy server. The GVL version of Cloudman is a popular
choice but there are many others. Please see: https://galaxyproject.org/use/

Best,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
https://usegalaxy.org
https://galaxyproject.org
https://galaxyproject.org/support
https://galaxyproject.org/learn
https://help.galaxyproject.org



On Mon, Aug 3, 2020 at 10:47 AM Xiaoshen Zhang 
wrote:

> Dear Galaxy team,
>
> Recently, I have been running TRINITY for RNA-seq data analysis, but the
> “my history” status always display the job is waiting to be run (the color
> never changed). When I implemented some analyses on galaxy, ONLY this
> method displayed “job waiting to be run” and nothing happened.
>
> After trying for several times and everything, I suppose something wrong
> with my account or the TRINITY method.
>
> Hope you can kindly fix this problem. Thanks for all the efforts you have
> been made. My account is exactly this email address.
> Details for TRINITY: (
> https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1
> )
>
> Best Regard,
>
> David
>
>
>
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[galaxy-dev] Re: Upload bed files seems to be hung

[Jennifer Hillman-Jackson]

Hi Jean,

This occurred at the public Galaxy Main server https://usegalaxy.org?

If so, this server is under heavy load, and even Upload jobs may queue for
a bit longer than usual. Allow all queued jobs to stay queued. Avoid
deleting and rerunning jobs with hopes of jobs running faster that way.
Rerunning loses the original job's queue placement and the new job is added
back to the end again, further extending wait time. Your jobs probably
completed by now, but if you need more help, please let us know.

Should you be working at a different Galaxy, know that most are also very
busy. But you can check with the server administrators to confirm. All
known public Galaxy servers are listed in the *Galaxy Platform Directory*.
Contact information is sometimes included in their directory listing and
sometimes on the server's home page itself: https://galaxyproject.org/use/.
If you cannot find it, write back and note the base URL of the server, and
we can try to help more.

Thanks for reporting the problem, and for your patience!

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
https://usegalaxy.org
https://galaxyproject.org
https://galaxyproject.org/support
https://galaxyproject.org/learn
https://help.galaxyproject.org



On Wed, May 27, 2020 at 8:59 AM Jean Jasinski 
wrote:

> I submitted 2 bed files for upload to Galaxy a couple of hours ago, and it
> shows "the job is waiting to run."  I have never had an upload take so
> long.  The status page said everything was working normally with no issues
> reported today.
>
> Is there an issue with the job queue or is the system just heavily loaded?
>
> Thanks,
> Jean Jasinski
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[galaxy-dev] Re: Deleted Galaxy Account

[Jennifer Hillman-Jackson]

Hello,

Please review and reply with your information on the *private* mailing
list. DO NOT reply to this *public* mailing list with your private
information.

https://help.galaxyproject.org/t/accounts-deleted-from-galaxy-main-to-enforce-posted-terms-and-conditions/1429/18?u=jennaj

FAQ: Getting an account at Galaxy Main (http://usegalaxy.org)
<https://galaxyproject.org/support/account/>

Thanks for understanding,

Jen

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Galaxy Application Support
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https://galaxyproject.org
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On Thu, Nov 14, 2019 at 4:47 PM Horstmann, Cullen M <
horstman...@live.missouristate.edu> wrote:

> Good evening,
>
> Upon trying to log onto my galaxy profile I received this message: "This
> account has been marked deleted, contact your local Galaxy administrator to
> restore the account." ​I was hoping I could re-gain access to this account
> because I have a lot of differential gene expression data on my account.
> Please let me know what I need to do to re-gain access at your earliest
> convenience.
>
> Kind Regards,
> Cullen Horstmann
> Missouri State University
> Master's in Biology
> Graduate Researcher | Kim Lab
> Teaching Assistant | Biology Department
>
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[galaxy-dev] Re: 2 accounts by mistake

[Jennifer Hillman-Jackson]

Hi Alison,

You have just one account at Galaxy Main https://usegalaxy.org, created
with the email address rattra...@gmail.com in 2017 and last logged into two
days ago. It contains ~ 34 GB of data.

So it seems this happened at a different public Galaxy server. Each is
administered independently. Usually, data retention policies are noted
somewhere on the home page of the server or at the bottom of the *User >
Saved Histories* page. Contact information is also usually on the home page
of the server and/or here: https://galaxyproject.org/use/

If you need help finding the contact info, share back the base URL of the
public Galaxy server and we can help you to find the contact info.

Thanks!

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
https://usegalaxy.org
https://galaxyproject.org
https://galaxyproject.org/support
https://galaxyproject.org/learn
https://help.galaxyproject.org



On Mon, Jul 22, 2019 at 7:41 AM Rattray, Alison (NIH/NCI) [C] via
galaxy-dev  wrote:

> I forgot that I had set up an account a while ago, but came across the old
> account tonight.  Problem is that as I was trying to merge them it seems
> all my files are now gone.  Neither of my sign in addresses gets me back to
> my data (ouch!).  How can I get beyond this.  (Yes I tried what is
> suggested when it says that my data is deleted... nothing shows up.  Would
> appreciate some input into how to merge my two accounts into one and
> hopefully rescue my data as well  Thank you
>
> Alison J. Rattray, Ph.D.
> Contractor
> RNA Biology Laboratory
> 1050 Boyles St.  Bldg 539 Rm 222
> Frederick, Maryland 21701
> (301)846-6715
> Cell 240-529-7172
> Alternative email:  rattra...@gmail.com
>
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Re: [galaxy-dev] Doubts about FTP upload.

[Jennifer Hillman-Jackson]

Hello,

The server name is *usegalaxy.org <http://usegalaxy.org>* (no ftp://
prefix).

Full FTP upload help is here: https://galaxyproject.org/ftp-upload/

Thanks!

Jen

--
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Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Wed, Apr 11, 2018 at 12:20 PM, Álvaro Rios <rios.alvaro1...@gmail.com>
wrote:

> Dear
>
> I am trying to upload files via FTP. However, the following message
> appears.
>
> "Authentication required ftp://usegalaxy.org Your connection to this site
> is not private." I do not have the experience to use galaxy, What I need to
> do?
>
> Thank you.
>
> Álvaro Rios.
>
>
>
>
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Re: [galaxy-dev] Problem with dependencies: Conda/freebayes

[Jennifer Hillman-Jackson]

Hello,

Did the suggested help from Biostars help?
https://biostar.usegalaxy.org/p/26197/

Thanks!

Jen

--
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http://biostar.usegalaxy.org


On Wed, Jan 3, 2018 at 6:01 AM, Matthias Enders <
m.end...@german-seed-alliance.de> wrote:

> Dear Galaxy Dev Mailing List,
>
> We encountered a problem while installing freebayes and its via Tool Shed.
>
> Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19); gawk
> (4.1.3) (all have the Current Installation Status "Installed through
> Conda") but then failed on the last dependency "parallel". (Status: "Not
> Installed")
>
> The strange thing is: parallel was installed correctly. Its callable from
> the command line, (e.g. parallel --help works fine) and installed with the
> latest version. But it's not recognized by Galaxy.
>
> We are using the Galaxy - Docker image in Version 17.09.
>
> Can you please assist us in resolving this?
>
> Mit freundlichen Grüßen
>
> Matthias Enders
> ---
>
>
> GERMAN SEED ALLIANCE GmbH
> c/o Norddeutsche Pflanzenzucht
> Hans-Georg Lembke KG
> Hohenlieth, 24363 Holtsee
> Tel.: +49 (0)4351/ 736-189
> Fax: + 49 (0)4351/ 736-271
> Mobil: +49 (0)151/ 14247360
>
> Email: m.end...@german-seed-alliance.de
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -Ursprüngliche Nachricht-
> Von: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im
> Auftrag von galaxy-dev-requ...@lists.galaxyproject.org
> Gesendet: Donnerstag, 21. Dezember 2017 18:00
> An: galaxy-dev@lists.galaxyproject.org
> Betreff: galaxy-dev Digest, Vol 138, Issue 9
>
> Send galaxy-dev mailing list submissions to
> galaxy-dev@lists.galaxyproject.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.galaxyproject.org/listinfo/galaxy-dev
> or, via email, send a message with subject or body 'help' to
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>
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>
> When replying, please edit your Subject line so it is more specific than
> "Re: Contents of galaxy-dev digest..."
>
>
> HEY!  This is important!  If you reply to a thread in a digest, please 1.
> Change the subject of your response from "Galaxy-dev Digest Vol ..." to the
> original subject for the thread.
> 2. Strip out everything else in the digest that is not part of the thread
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>
> Why?
> 1. This will keep the subject meaningful.  People will have some idea from
> the subject line if they should read it or not.
> 2. Not doing this greatly increases the number of emails that match search
> queries, but that aren't actually informative.
>
> Today's Topics:
>
>1. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo)
>
>
> --
>
> Message: 1
> Date: Wed, 20 Dec 2017 13:52:45 -0600
> From: Ping Luo <luop0...@gmail.com>
> To: Hans-Rudolf Hotz <h...@fmi.ch>
> Cc: galaxy-dev <galaxy-dev@lists.galaxyproject.org>
> Subject: Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work
> Message-ID:
> <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=ADoyw@mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hans-Rudolf,
>
> I just started a brand new galaxy with the default internal database. I
> did the minimal change to galaxy.ini so that I could use CAS authentication.
> Still, impersonation failed.
>
>
> Ping
>
> On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>
> > Hi Ping
> >
> >
> > Does it work with a fresh installation ( v17.09) staring with an empty
> > PostgrSQL database?
> >
> >
> > Hans-Rudolf
> >
> > On 12/19/2017 03:41 PM, Ping Luo wrote:
> >
> >> Hans-Rudolf,
> >>
> >> Yes, I have set the flag to be true
> >>
> >>  # Allow administrators to log in as other users (useful for
> >> debugging)
> >>  allow_user_impersonation = True
> >>
> >> We use CAS authentication and our database is Postgresql. Our current
> >> Galaxy is v15.07 and impersonation works well. I have tried v16.10
> >> before and impersonation didn't work either.
> >>
> >> Thanks,
> >>
> >> Ping
> >>
> >> On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz <h...@fmi.ch
> >

Re: [galaxy-dev] genome upload

[Jennifer Hillman-Jackson]

Hello Marion,

To use this genome immediately, it is best to use it as a *custom reference
genome*. This is how: https://galaxyproject.org/learn/custom-genomes/

To have it reviewed for inclusion at Galaxy Main as a natively indexed
genome, please add a comment to this master genome request ticket. Include
the build details and a link to a public repository (NCBI, etc) that hosts
the genome data. Details here:
https://github.com/galaxyproject/galaxy/issues/1470

Thanks!

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Tue, Jul 25, 2017 at 8:34 AM, Marion Cerri <marion.ce...@lmu.de> wrote:

> To whom it concerns,
> I am Marion Cerri, post doc in the Parniske’s lab, in Munich. I am working
> with ChIP-seq data in the moment.
> I would like to use the Lotus japonicus (version 3.0) for mapping reads,
> but the genome is not available on galaxy. Would it be possible to upload
> it ? Do I have to provide the file to you, and if so in fasta format ?
> Thanks in advance
> Best Regards
> Marion Cerri
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[galaxy-dev] Release of Galaxy 17.05

[Jennifer Hillman-Jackson]

Dear Galaxy Fans,

We are pleased to announce the *release of Galaxy 17.05*. Thanks to the
#usegalaxy committers and you, our community!


Full release notes:

https://docs.galaxyproject.org/en/master/releases/17.05_announce.html


Highlights:
*Tag your data with propagating hashtags*

Large Galaxy histories used to be messy. Hashtags make it easy to track
dataset (and collection) relationships. These two movies (both under a
minute) explain how to use this with datasets 
 and with collections .

Learn more about Galaxy histories in our updated tutorial

*Drag & Drop datasets into tool inputs*Interface now allows dragging
datasets from history panel into the content selectors of the tool form.
Implemented in Pull Request 3871
.*Upload directly to a
collection*

You can now bypass the history manipulation and upload your data straight
into a collection for convenience.

Learn more about collections and how to use them in a new tutorial
.

We extend special thanks to the 64 New Contributors

to
Galaxy in the past year.

*Thanks for using Galaxy!*

*http://galaxyproject.org *
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[galaxy-dev] Fwd: Galaxy on the Amazon cloud

[Jennifer Hillman-Jackson]

-- Forwarded message --
From: Матвей Спринджук 
Date: Wed, Feb 15, 2017 at 1:01 AM
Subject: Galaxy on the Amazon cloud



Are there any guidelines and tutorials on how to tune Galaxy instance in
the Amazon cloud environment?

We need to know how to set up .ini  and .xmls files in details. I have read
all the documentation which is available.

We have one fresh Galaxy instance at https://genomics.tbportal.org/galaxy/
and struggling on setting it up properly.



Thank you and your Team

Matvey Sprindzuk, computer/biomedical scientist, MD

Belarus, Minsk, UIIP

+375 29 567 10 73 <+375%2029%20567-10-73>
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Re: [galaxy-dev] Galaxy Orione server name

[Jennifer Hillman-Jackson]

Hello Blaise,

The URL to use for FTP is the same as the base URL for the website. For
this Galaxy instance, use this as the server name: *orione.crs4.it
<http://orione.crs4.it>*

https://wiki.galaxyproject.org/PublicGalaxyServers#Orione

Best,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
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http://galaxyproject.org
http://biostar.usegalaxy.org


On Tue, Dec 6, 2016 at 8:36 AM, Blaise Pascal Bougnom <
b.p.boug...@bham.ac.uk> wrote:

> Dear,
>
> Please you give me the server name of Galaxy Orione?, It is to upload my
> file via FTP.
>
> Best wishes
>
>
>
> Dr Blaise Bougnom
>
> b.p.boug...@bham.ac.uk <r.hu...@bham.ac.uk>
> [image: cid:image001.jpg@01CDC96B.45E56E80]
> Antimicrobials Agents Research Group
> Institute of Microbiology and Infection
> Room S110, Biosciences Building
> Edgbaston
> Birmingham B15 2TT
> Tel: 012141 58693
> Mob: 075031 65000
>
>
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Re: [galaxy-dev] There is a bug in Lefse system

[Jennifer Hillman-Jackson]

Hello,

Perhaps try contacting the lab directly to see if there are known issues?

https://wiki.galaxyproject.org/PublicGalaxyServers#Huttenhower_Lab

Thanks!

Jen

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Galaxy Application Support
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On Thu, Oct 13, 2016 at 11:13 AM, Bueno Silva,Carla Grazielle <
cbuenosi...@ufl.edu> wrote:

> Hi!
>
> I'm trying to upload my data in Lefse system, but it show this message: 
> "Failed:
> Bad Request (400)"
>
> Yesterday I tried and I could upload these files, but today I can not upload 
> the same files.
> I think it's a problem in the website.
>
> Could you please help me?
>
> Thank you! =)
>
> Carla.
>
>
>
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Re: [galaxy-dev] sending data

[Jennifer Hillman-Jackson]

Hello,

Galaxy accepts data using *passive FTP*. This client will send data that
way but also in various secure modes. Please try using passive mode.

Thanks!

Jen

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Galaxy Application Support
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On Tue, Aug 16, 2016 at 7:27 AM, Labdros drosophila <labdrosgal...@gmail.com
> wrote:

> In the last two days I'm dificuldaddes techniques to send my data by BAREFTP 
> , I wanted to know if there is anything wrong by port 21 or the server?
>
> Thank you for your attention and sorry for any inconvenience.
>
>
>
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Re: [galaxy-dev] Doubts about Galaxy installation.

[Jennifer Hillman-Jackson]

Hello,

This wiki will address your questions: http://getgalaxy.org

If you do need specific help with an operation after trying it, the
community can help. Include details about the issue and leave the mailing
list on the cc.

Thanks,

Jen

--
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Galaxy Application Support
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http://galaxyproject.org
http://biostar.usegalaxy.org


On Sun, Jun 26, 2016 at 5:08 PM, Álvaro Rios <rios.alvaro1...@gmail.com>
wrote:

> Dear Member of the Galaxy Team,
>
>
>
> My name is Álvaro Rios, I am Associate Professor of the North Fluminense
> State University, RJ, Brazil. I am a beginner in the use of Galaxy tools
> and, I would like to install my own Galaxy.
>
> However I am not familiarized with command lines for instation of Galaxy.
> My interest is to use tool like BS-seeker2 avaible into Toolshed. I am
> using a MacBook Pro (2,2 GHz Intel Core i7; 16G RAM). It is enough to work
> with Galaxy?
>
> I saw that I can download a zipped file version and install it. What file
> I need to click to install Galaxy?
>
> How can I become a administrador?
>
> Thank you for your attention,
>
> With Best Regards
>
> Álvaro Rios.
>
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Re: [galaxy-dev] a quick question about picard

[Jennifer Hillman-Jackson]

Hello,

A Data Manager for this function exists in the Tool Shed. Perhaps it will
help with troubleshooting?

https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_picard_index_builder/00491eabe22b

Best,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Fri, Apr 29, 2016 at 2:09 PM, Beginner TI <ruiwang...@gmail.com> wrote:

> Hi All,
>
> I wrote a very simple wrapper for one picard function. Here is the xml
> file:
>
>  version="1.126.0">
>   Create Sequence Dictionary
>   
> picard
>   
>
>   
> picard_macros.xml
>   
>
>   
> @java_options@
> java -jar \$JAVA_JAR_PATH/picard.jar
> CreateSequenceDictionary
> R="${ref_file}"
> O="${dict_file}"
>   
>   
> 
>   
>   
> 
>   
>   
> **Purpose**
> Create Sequence Dictionary from fa file
>   
> 
>
> It's ugly, I know. :-( Just want to finish a quick test...however when I
> tried to run a test, it always says something like:
>
> Exception in thread "main" picard.PicardException: 
> /media/4tb-ext/galaxy-data-store/database/files/008/dataset_8757.dat already 
> exists.  Delete this file and try again, or specify a different output file
>
> When I looked at that file, it has a size 0, but even I remove that file, 
> I'll still see the same thing.
>
> Galaxy terminal executes:
>
> galaxy.jobs.runners.local DEBUG 2016-04-29 13:55:51,423 (3189) executing: 
> GALAXY_SLOTS="1"; export GALAXY_SLOTS; 
> _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && export 
> _JAVA_OPTIONS &&   java -jar $JAVA_JAR_PATH/picard.jar 
> CreateSequenceDictionary R="/media/mybook/GATK_galaxyWrapper/hg38.fa" 
> O="/media/4tb-ext/galaxy-data-store/database/files/008/dataset_8757.dat"
>
> Seems it did the right thing, but why that set_meta set state to ERROR? Oh 
> there was indeed a warning:
>
> WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with 
> extension 'eset', using datatype from 
> /media/4tb-ext/galaxy-data-store/database/tmp/tmp_Uuw5Y.
>
> Have anyone seen this before? I'm quite confused since the same commandline 
> runs smoothly in the terminal.
>
> Thanks,
>
> Rui
>
>
> ___
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Re: [galaxy-dev] Adding Reference genome of Chicken and Duck in Tophat

[Jennifer Hillman-Jackson]

Hi Vijay,

Chicken will be added soon. Duck needs a review first. I'll put more
comments in your Biostars post later today/tomorrow depending on progress
for galGal3/4.

https://biostar.usegalaxy.org/p/17529/

Thanks,



Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Sat, May 7, 2016 at 6:08 AM, Vijay Kumar <nayaganv...@gmail.com> wrote:

> Dear sir,
> Kindly add reference Genome of Chicken (Gallus gallus) and Duck (Anas
> platyrhynchos) in Tophat Reference genome section.
> *Regards,*
> *Dr. P. Vijayakumar,*
> *Assistant Professor,*
> *Instructional Livestock Farm Complex, *
> *Veterinary College and Research Institute,*
> *Orathanadu, **Thanjavur,*
> *Tamil Nadu,*
> *India- 614625*
>
> ___
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>
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Re: [galaxy-dev] novice galaxy user needs help retrieving MIA history

[Jennifer Hillman-Jackson]

Hello Ryan,

Try finding it this way as a first step:

https://wiki.galaxyproject.org/Support#Example:_My_History_is_missing.21

Thanks,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Mon, Apr 18, 2016 at 7:20 PM, ryan stueve <jnkacc...@outlook.com> wrote:

> Greetings,
>  I am a novice Galaxy user. I was getting along perfectly this
> morning (made some mistakes, deleted some steps) and got to alignment steps
> in my RNAseq analysis. Went to some afternoon meetings, returned & logged
> back in- MY HISTORY WAS EMPTY!
>
> can you advise?
>
> Instance: MAIN/public
> Username/email: jnkacc...@outlook.com
> History name: something like "LUAD RNA-seq"; definitely had "LUAD" in title
>
> also, here is one of the steps/filenames that should be in history (I
> downloaded before meeting):
> "Galaxy240-[H1648_TopHat_on_data_164_and_data_163__accepted_hits].bam"
>
>
> any help sincerely appreciated
>
> ___
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> and other Galaxy lists, please use the interface at:
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>
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>
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Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from etiennewa...@yahoo.fr (megablast_wrapper)

[Jennifer Hillman-Jackson]

Hi Etienne,

Sorry, I didn't notice that the job was run on the test server.

The root of the problem could be that the job output exceeds quota. Running
the job there will not get around quota, even if the tool has other issues
on test that are triggering the failure (is possible - we do test on that
server).  If the tool did run, and the output hits your account, if it is
over quota (10 GB) no more jobs will be permitted to run.

It might be best to consider using a local or cloud Galaxy. I do not know
when the Fetch Taxonomy tool will be restored to Main (or if yet).

Thanks,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Thu, Mar 31, 2016 at 9:08 PM, etienne waleckx <etiennewa...@yahoo.fr>
wrote:

> Gracias Jenifer,
>
> I re-ran the tool but the same happens. It is strange as when running the
> same tool with the same file in usegalaxy it is working well but I can't in
> testgalaxy.
> I want to run it in testgalaxy so I can use the fetch taxonomic
> representation tool after. I already have the Megablast file but I can't
> upload it directly to testgalazxy as it semms too big, so I would like to
> run the megablast in testgalaxy, then fetch taxonomic representtion.
>
> Thanks for your help!
>
> Etienne
>
>
>
>
> --
> *De :* Jennifer Hillman-Jackson <j...@galaxyproject.org>
> *À :* "galaxy-b...@bx.psu.edu" <galaxy-b...@bx.psu.edu>
> *Cc :* etiennewa...@yahoo.fr
> *Envoyé le :* Jeudi 31 mars 2016 18h03
> *Objet :* Re: [galaxy-bugs] Galaxy tool error report from
> etiennewa...@yahoo.fr (megablast_wrapper)
>
> Hello,
>
> Please re-run the tool as this was most likely a transient cluster failure.
>
> Our apologies for any confusion,
>
> Jen
>
> --
> Jennifer Hillman-Jackson
> Galaxy Application Support
> http://usegalaxy.org
> http://galaxyproject.org
> http://biostar.usegalaxy.org
>
>
> On Wed, Mar 30, 2016 at 11:09 PM, <galaxy-b...@bx.psu.edu> wrote:
>
>
> GALAXY TOOL ERROR REPORT
> 
>
> This error report was sent from the Galaxy instance hosted on the server
> "https://test.galaxyproject.org/;
>
> -
> This is in reference to dataset id 763833 (c5a49985053f8bd3) from history
> id 328501 (aa1b4cb871c5e196)
>
> -
> You should be able to view the history containing the related history item
> (83ca2a7d5534e19e)
>
> 2: Megablast on data 1
>
> by logging in as a Galaxy admin user to the Galaxy instance referenced
> above
> and pointing your browser to the following link.
>
> https://test.galaxyproject.org/history?id=aa1b4cb871c5e196
>
> -
> The user 'etiennewa...@yahoo.fr' provided the following information:
>
> Hi,
>
> Can you help me? I don't find why the tool is not running with this
> dataset,
>
> Thanks!
>
> Etienne
>
> -
> info url:
> https://test.galaxyproject.org/datasets/83ca2a7d5534e19e/show_params
> job id: 529174 (5c8c4452f3c278b5)
> tool id:
> toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0
> tool version: 1.2.0
> job pid or drm id: 529174
> job tool version: None
>
> -
> job command line:
> None
>
> -
> job stderr:
>
>
> -
> job stdout:
>
>
> -
> job info:
> Remote job server indicated a problem running or monitoring this job.
>
> -
> job traceback:
> None
>
> -
> (This is an automated message).
>
>
>
>
>
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Re: [galaxy-dev] file transference between different galaxy servers...

[Jennifer Hillman-Jackson]

Opps, that should be "control-click" on a MAC OSX - sorry!

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Wed, Mar 30, 2016 at 10:10 AM, Jennifer Hillman-Jackson <
j...@galaxyproject.org> wrote:

> Hi Danilo,
>
> 1. Copy the URL for the dataset: option+click on the disc icon and choose
> "Copy Link Address"
> 2. Paste the URL into the Upload tool form: Paste/Fetch data
>
> Many can be done at once. Copy/paste the URLs into a temporary text file
> first, one per line, then copy/paste into the upload form.
>
> Thanks!
>
> Jen
>
> --
> Jennifer Hillman-Jackson
> Galaxy Application Support
> http://usegalaxy.org
> http://galaxyproject.org
> http://biostar.usegalaxy.org
>
>
> On Wed, Mar 30, 2016 at 4:38 AM, Danilo Ceschin <danilocesc...@gmail.com>
> wrote:
>
>> hi,
>> I have some big files uploaded at
>> galaxy.ncgas-trinity.indiana.edu
>> and I would like to use those file at
>> https://usegalaxy.org/
>> Is there a way to transfer those files to avoid upload them again? My
>> internet connection is very bad and it takes days just for one file.
>> Thank in advance.
>> sincerely yours,
>>
>> --
>> Danilo Ceschin PhD
>> Fac. de Ciencias Agrarias
>> IBAC - Instituto de Biotecnología Agropecuaria del Comahue
>> Ruta 151 - Km 12,5
>> CP 8303 - Cinco Saltos - Río Negro
>> Argentina
>>
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>  https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/mailinglists/
>
>
>
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Re: [galaxy-dev] Data set too large

[Jennifer Hillman-Jackson]

Hello,

FTP is needed for files over 2 GB by default. Try FTP upload. Please
contact your campus administrator if FTP is not enabled. Your admin is the
best resource for alternatives if FTP is not active and will not be (admin
loads data into libraries, and the like).

https://wiki.galaxyproject.org/Support#Loading_data

Please note that the target FTP server is usually the same as the
instance's base URL and the credentials (email/pass) are the same as for
your Galaxy account on that instance. This information is unique for every
Galaxy instance. Try using Filezilla if you are not comfortable with FTP on
the command line.

Take care,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Wed, Mar 23, 2016 at 4:28 PM, Tiara Smith <tiara.y.sm...@gmail.com>
wrote:

> Hell I am accessing galaxy from a main computer on my university campus. I
> am having difficulty uploading my exome files and keep getting the
> following error prompt:
>
> ndex30_CACCGG_L001-L002_R1_001.bam
> *2.8* GB
> Auto-detect
>
> - Additional Species Are Below -
> *Failed: *File exceeds 2GB. Please use a FTP client.
>
>
>
> Is there a way to increase my file upload limit? my data sets range from
> 1.9GB ro 3.9GB.
>
>
> thank you for your help.
>
> Tiara Smith
>
> ___
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>
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Re: [galaxy-dev] REGISTRATION OF GALAXY

[Jennifer Hillman-Jackson]

Hello,

If you want an account at http://usegalaxy.org, these are the instructions:
https://wiki.galaxyproject.org/Support#Getting_an_account

If you want an account at another site, please contact the server's
administrator.

Thanks,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Fri, Feb 12, 2016 at 6:30 AM, martin perez <martinp...@hotmail.com>
wrote:

> Hello;
>
>
>
> How are you, I am from Panamá i try registrer for Galaxy /galaxeast, program
> but i dont know as do.
>
>
>
> Do you can help me?
>
> I am student in the university.
>
>
>
> Martin Perez
>
> Panamá, Panamá.
>
>
>
>
>
> ___
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>
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Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

[Jennifer Hillman-Jackson]

Hi Felix,

I have recalculated disk for you again. Our team is aware of this problem
and is working on a more permanent solution.

We will take a look at your workflow/histories to rule out a tool or
workflow function problem. If this does turn out to be a method issue
instead, then contacting the authors of the Cloudman pipeline would be
recommended as the next step. https://usegalaxy.org/u/gm2123/p/cloudmap

Thanks for using Galaxy and we will get back to you in a bit about the
workflow,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Tue, Dec 1, 2015 at 12:45 AM, Felix Mayr <fm...@age.mpg.de> wrote:

> The login emailaddress I use is felix.m...@gmail.com.
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
> On 01 Jan 2015, at 09:44, Felix Mayr <fm...@age.mpg.de> wrote:
>
> Dear Galaxy dev,
>
> I have two problems, which might be related to each other.
>
> 1) For a long time already, I continuously have ‘left over’ data
> allocation after deleting and purging histories. Someone from your team has
> repeatedly resolved that problem, but it root of the problem still
> persists. I know have 91% allocation, when only having two histories of
> 67.48 and 59.45 GB.  The fix for automatic recalculation doesn’t seem to
> work…?
>
> 2) I recently performed SNP mapping using a CloudMap based pipeline. The
> problem: the SNP mapping plots shows the exact same mapping/plots of the
> SNPs. They can not be the same. What is not the problem: the input files,
> as they are different in size, first and last lines of the files, and they
> produce very different SNP mapping mutation tables. Therefore, I think
> there might be a problem that the workflow somehow uses the same
> intermediate file for generating the SNP mapping plots. I already
> re-uploaded and rerun the workflows in new histories multiple times, but
> the same result each time. I would upload and run another data set for
> which I already have SNP mapping plots to see whether I again get the same
> plots or not, but that is now not possible as I am close to the data quota.
>
> I hope you can help solve these problems.
>
> All best,
>
> Felix
>
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
>
>
> ___
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> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] Turn your workflow into a tool?

[Jennifer Hillman-Jackson]

Hello,

Go the the Worflows home page by clicking on the link in the upper
masthead. On the bottom of that page, in the section 'Other options' click
on the button 'Configure your workflow menu'.

The next page lists all of your workflows. To place any at the top of your
workflow list (found at the bottom of the left tool panel in the 'Analyze
Data' view), mark the checkbox in the column 'Show in menu'.

All workflows are listed by default in the tool panel now, this just
promotes the checked workflows to the top, where they can be quickly
accessed and used "like a tool".

A bit more customization can be done, such as hiding intermediate workflow
steps so that just the result dataset is active in the history. Do this in
the workflow editor.

Thanks for using Galaxy,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Tue, Sep 1, 2015 at 5:37 PM, Alexander Vowinkel <
vowinkel.alexan...@gmail.com> wrote:

> Hi,
>
> this page:
> https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/ToolPanel
>
> is linked here:
> https://wiki.galaxyproject.org/Learn/AdvancedWorkflow
>
> but does not exist.
>
> How can I put my Workflow for all users into the Tool Panel?
>
> Thanks,
> Alexander
>
>
> ___
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>
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>   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] about galaxy

[Jennifer Hillman-Jackson]

Hello,

The datatype 'fastqsanger' needs to be assigned. See the Galaxy Support
wiki for how to do this (and for how to double check if the type is
correct):
https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

Thanks for using Galaxy,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Wed, Sep 2, 2015 at 8:29 AM, Dong Liu <dl1...@uga.edu> wrote:

> Dear Galaxy
>
> I am a new user on Galaxy online service. When I uploaded my data file in
> fastq form, the utility of Galaxy such as NGS:QC and manipulation, FastQC
> and Trim sequences can not be availabe. I dont why. can you tell me how to
> use Galaxy using my data?
>
>
>
> Dong Liu
>
>
>
> visiting scholar at the University of Georgia,GA, USA
>
> ___
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>
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Re: [galaxy-dev] Turn your workflow into a tool?

[Jennifer Hillman-Jackson]

Hi Alexander,

Thanks for the reminder to get that info posted - is about 95% done. Plus I
decided just now to add a bit about sharing to this same page. I'll have
this part done tomorrow, and will work on getting the rest of this wiki
area polished near term (updates + unpublished tutorials).

For the question, your own workflows are not automatically shared with
other users. But workflows can be shared just like histories, pages, and
visualizations with other users working on the same Galaxy instance.

Click into "Workflow" on the masthead, then click on the workflow name. The
menu has a sharing option. To share with everyone, publish it. This will
make it visible under "Shared Data -> Published Workflows" in the masthead.
A description of how it works is in the wiki here:
https://wiki.galaxyproject.org/Learn/Share

Take care,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Wed, Sep 2, 2015 at 12:56 PM, Alexander Vowinkel <
vowinkel.alexan...@gmail.com> wrote:

> awesome! that worked!
> Now I can also see the Page ;)
>
> Will such a shown workflow be visible for all users?
> If not, is is possible to make it visible to all users?
>
> Thanks,
> Alexander
>
> 2015-09-02 12:02 GMT-05:00 Jennifer Hillman-Jackson <j...@galaxyproject.org
> >:
>
>> Hello,
>>
>> Go the the Worflows home page by clicking on the link in the upper
>> masthead. On the bottom of that page, in the section 'Other options' click
>> on the button 'Configure your workflow menu'.
>>
>> The next page lists all of your workflows. To place any at the top of
>> your workflow list (found at the bottom of the left tool panel in the
>> 'Analyze Data' view), mark the checkbox in the column 'Show in menu'.
>>
>> All workflows are listed by default in the tool panel now, this just
>> promotes the checked workflows to the top, where they can be quickly
>> accessed and used "like a tool".
>>
>> A bit more customization can be done, such as hiding intermediate
>> workflow steps so that just the result dataset is active in the history. Do
>> this in the workflow editor.
>>
>> Thanks for using Galaxy,
>>
>> Jen
>>
>> --
>> Jennifer Hillman-Jackson
>> Galaxy Application Support
>> http://usegalaxy.org
>> http://galaxyproject.org
>> http://biostar.usegalaxy.org
>>
>>
>> On Tue, Sep 1, 2015 at 5:37 PM, Alexander Vowinkel <
>> vowinkel.alexan...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> this page:
>>> https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/ToolPanel
>>>
>>> is linked here:
>>> https://wiki.galaxyproject.org/Learn/AdvancedWorkflow
>>>
>>> but does not exist.
>>>
>>> How can I put my Workflow for all users into the Tool Panel?
>>>
>>> Thanks,
>>> Alexander
>>>
>>>
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>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
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[galaxy-dev] May 2015 Galaxy Release (v 15.05)

[Jennifer Hillman-Jackson]

*The May 2015 Galaxy Release is out!*

Release Notes v 15.05
http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html

Release Highlights

   -

   *Authentication Plugins* - Galaxy now has native support for LDAP and
   Active Directory via a new community developed authentication plugin system.
   -

   *Tool Sections* - Tool parameters may now be groupped into collapsable
   sections.
   -

   *Collection Creators* - New widgets have been added that allow much more
   flexibility when creating simple dataset pair and list collections.
   -

   And *much more
   http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html*

The release notes have a new home at Read the Docs
http://galaxy.readthedocs.org/en/master/releases/15.05_announce.html. We
hope that you like the new format as much as we do! *Thanks for using
Galaxy! *
The Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam


--

Registration for the 2015 Galaxy Community Conference is OPEN!
http://gcc2015.tsl.ac.uk

*Love* *Galaxy*? We are inviting Galaxy power end-users as well as
scientists and bioinformatics support researchers to *join us for the
inaugural* *Galaxy Data Wrangling Hackathon* preceding the 2015 Galaxy
Community Conference conference this July.
http://gcc2015.tsl.ac.uk/data-hackathon
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Re: [galaxy-dev] error in Galaxy (lefse)

[Jennifer Hillman-Jackson]

Hi Luigi,

Is this the public Galaxy server in use? If so, please contact the team
that administrates the instance directly. The contact information is in the
link.
http://wiki.galaxyproject.org/PublicGalaxyServers#Huttenhower_Lab

The advice is true for all public Galaxy servers presenting with problems
not supported by the core team (Main: http://usegalaxy.org and Test:
https://test.galaxyproject.org). Just keep in mind that Test really is a
test server. Various errors at unpredictable times should be expected -
meaning, it is best to not use Test for critical work.

Should you be using the version of the tool from the Main Tool Shed (
http://usegalaxy.org/toolshed) in a local or cloud Galaxy, contact the
administrator of that instance. If this is a server that you run yourself,
I can let you know that the error tends to be related to high server load
and/or insufficient resources. Often it will go away after a few minutes if
the issue really is peak database-load. Has the tool ever run successfully
on your server? If not, consider moving to a PostgreSQL database if you
have not already (instead of the default SLQlite). If the tool will run
line-command with the available resources, it should almost certainly run
in Galaxy with the correct configuration. Just in case you need it, these
are the production database set up instructions. More is in the Admin hub
of the wiki.
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server

Thanks,
Jen
Galaxy team

On Fri, Apr 24, 2015 at 4:41 AM, Borruso Luigimaria 
luigimaria.borr...@unibz.it wrote:

  Dear Galaxy-project staff,

 in the last two weeks, I have tried several time to use Lefse but it seems
 to have some problem. I always get the following message:


 * Internal Server Error Galaxy was unable to successfully complete your
 request. An error occurred. This may be an intermittent problem due to load
 or other unpredictable factors, reloading the page may address the problem.
 The error has been logged to our team. Thanks a lot *

 Luigi Borruso, PhD
 Environmental Microbiology

 Faculty of Science  Technology
 Building K, Office 1.05
  Free University of Bozen/Bolzano
 Piazza Università 5
 I-39100 Bozen/Bolzano
 Italy

 Tel. +39 0471 017610
  E-mail: luigimaria.borr...@unibz.it lorenzo.bruse...@unibz.it
 Website: www.unibz.it/sciencetechnology



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-- 
Jennifer Hillman-Jackson
http://galaxyproject.org
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[galaxy-dev] March 2015 Galaxy Release (v 15.03)

[Jennifer Hillman-Jackson]

*March 2015 Galaxy Release (v 15.03)*
https://wiki.galaxyproject.org/News/2015_03_GalaxyRelease

[image: width=175] http://getgalaxy.org/

Complete Release Notes http://wiki.galaxyproject.org/DevNewsBriefs/2015_03


Highlights

   -

   *Release Versioning
   https://wiki.galaxyproject.org/DevNewsBriefs/2015_03#Release_Versioning*
   -

  Starting with this distribution, an updated Galaxy release versioning
  system has been implemented. The versioning scheme is Ubuntu-style
  https://wiki.ubuntu.com/Releases.

   *Github https://wiki.galaxyproject.org/DevNewsBriefs/2015_03#Github*
   - Galaxy development has moved to Github, but stable/release changes are
  mirrored to Bitbucket. Deployers can continue to use Bitbucket
as they have
  done in the past. Release branches discussed in the full release notes.

   *Tool Redesign
   https://wiki.galaxyproject.org/DevNewsBriefs/2015_03#Tool_Redesign*
   -

  Much of Galaxy’s core tool set has been redesigned. Several contain
  new functionality. These tools are included in the Tool Shed
  http://usegalaxy.org/toolsehd and many are ready for use on Galaxy
  Main https://wiki.galaxyproject.org/Main.

Get the Galaxy Release

[image: getgalaxy] http://getgalaxy.org/

*getgalaxy.org http://wiki.galaxyproject.org/Admin/Get%20Galaxy*

*galaxy-dist.readthedocs.org http://galaxy-dist.readthedocs.org/*

*bitbucket.org/galaxy/galaxy-dist http://bitbucket.org/galaxy/galaxy-dist*

*new*:

$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

*upgrade*:

$ hg pull
$ hg update latest_15.03



*Thanks for using Galaxy!*
The Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: [galaxy-dev] TopHat error

[Jennifer Hillman-Jackson]

Hello,

I would start by confirming the SAMTools indexes and tool installs. Confirm
that you can execute SAMTools tool's successfully within Galaxy. If there
are problems, check to see if there is a PATH issue. Make sure the galaxy
user is accessing the correct version (and indexes for reference genomes
used). If you are using a cluster, then confirm the tools/indexes are
configured correctly there, too.

Hopefully this helps,
Jen
Galaxy team

On Mon, Mar 9, 2015 at 8:08 AM, Scott Szakonyi scott.b.szakony...@nd.edu
wrote:

 Hello all,

 I have a user who is getting the following error when analyzing a FASTQ
 file using TopHat for Illumina.

 TopHat v2.0.10
 [bam_header_read] EOF marker is absent. The input is probably truncated.
 [bam_header_read] invalid BAM binary header (this is not a BAM file).
 [bam_index_core] Invalid BAM header.
 [bam_index_build2] fail to index the BAM file.
 Error indexin


 I've tried reloading the tool and all it's dependencies, to no avail.
 We've been able to run the same FASTQ file successfully on another Galaxy
 server with identical tool configuration. I'm out of ideas, being
 relatively new to Galaxy. Has anyone seen a similar error? Can you offer an
 possible solutions?

 Thanks!

 --
 Scott B. Szakonyi
 Research Programmer

 *Center for Research Computing*
 107 Information Technology Center
 Notre Dame, IN 46556
 http://crc.nd.edu

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-- 
Jennifer Hillman-Jackson
http://galaxyproject.org
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[galaxy-dev] January 13, 2015 Galaxy Distribution

[Jennifer Hillman-Jackson]

*January 13, 2015 Galaxy Distribution*
https://wiki.galaxyproject.org/News/2014_01_13_Galaxy_Distribution
[image: width=175] http://getgalaxy.org/
*Complete News Brief
http://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13*

Security

Several *critical* security vulnerabilities were recently discovered by
Bartlomiej Balcerek and colleagues at the Wroclaw Centre for Networking and
Supercomputing. This stable Galaxy release contains fixes for those
vulnerabilities
https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#Security. *The
Galaxy Team strongly encourages Galaxy server administrators to update
their Galaxy servers immediately.*

IPython Integration
Thanks to the awesome work of community members Björn Grüning and Eric
Rasche, Galaxy now features integration with the popular IPython project
https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#IPython_Integration.
The Galaxy-IPython https://github.com/bgruening/galaxy-ipython project
has been merged into Galaxy core and made into a generic plugin framework
of interactive environments based on Docker.

Tool Form Upgrade (for Beta Testing)
In Galaxy's development branch, the basic tool from has been redesigned and
modernized to address certain limitations in Galaxy's responsiveness when
working with longer forms containing multiple parameter choices
https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#Tool_Form_Upgrade_.28for_Beta_Testing.29.
This new tool form will become the default with the next release - but we
are hoping tool author's and power users enable it and provide feedback
during this release cycle in order to ensure it is working ideally when it
becomes the default.

Get The Distribution

[image: getgalaxy] http://getgalaxy.org/

*getgalaxy.org http://wiki.galaxyproject.org/Admin/GetGalaxy*

*galaxy-dist.readthedocs.org http://galaxy-dist.readthedocs.org/*

*bitbucket.org/galaxy/galaxy-dist http://bitbucket.org/galaxy/galaxy-dist*

*new*:

$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

*upgrade*:

$ hg pull
$ hg update latest_2015.01.13



*Thanks for using Galaxy!*
The Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam


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