[galaxy-dev] January 13, 2015 Galaxy Distribution

!* The Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- Jennifer Hillman-Jackson http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy

[galaxy-dev] March 2015 Galaxy Release (v 15.03)

://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 ___ Please

Re: [galaxy-dev] TopHat error

reply all 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/ -- Jennifer Hillman-Jackson

Re: [galaxy-dev] error in Galaxy (lefse)

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 in your mail client. To manage your subscriptions

[galaxy-dev] May 2015 Galaxy Release (v 15.05)

*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

Re: [galaxy-dev] Turn your workflow into 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://galaxyprojec

Re: [galaxy-dev] about galaxy

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

Re: [galaxy-dev] Turn your workflow into a tool?

e 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-Jac

Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

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

Re: [galaxy-dev] Doubts about Galaxy installation.

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 -- Jennifer Hillman-Jackson Galaxy Application Support

Re: [galaxy-dev] REGISTRATION OF GALAXY

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

Re: [galaxy-dev] file transference between different galaxy servers...

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&

Re: [galaxy-dev] Data set too large

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 ga

Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from etiennewa...@yahoo.fr (megablast_wrapper)

-- 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

Re: [galaxy-dev] Adding Reference genome of Chicken and Duck in Tophat

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

Re: [galaxy-dev] a quick question about picard

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

Re: [galaxy-dev] novice galaxy user needs help retrieving MIA history

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

[galaxy-dev] Fwd: Galaxy on the Amazon cloud

-- 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

Re: [galaxy-dev] sending data

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

Re: [galaxy-dev] There is a bug in Lefse system

Hello, Perhaps try contacting the lab directly to see if there are known issues? https://wiki.galaxyproject.org/PublicGalaxyServers#Huttenhower_Lab Thanks! Jen -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org

Re: [galaxy-dev] Galaxy Orione server name

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 Appli

Re: [galaxy-dev] genome upload

. 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

[galaxy-dev] Release of Galaxy 17.05

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

Re: [galaxy-dev] Problem with dependencies: Conda/freebayes

Hello, Did the suggested help from Biostars help? https://biostar.usegalaxy.org/p/26197/ Thanks! Jen -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org On Wed, Jan 3, 2018 at 6:01 AM, Matthias Enders < m.

Re: [galaxy-dev] Doubts about FTP upload.

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

[galaxy-dev] Re: 2 accounts by mistake

are 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 ht

[galaxy-dev] Re: Deleted Galaxy Account

an account at Galaxy Main (http://usegalaxy.org) <https://galaxyproject.org/support/account/> Thanks for understanding, Jen -- Jennifer Hillman-Jackson Galaxy Application Support https://usegalaxy.org https://galaxyproject.org https://galaxyproject.org/support https://galaxyproject.org/learn

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

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

[galaxy-dev] Re: Upload bed files seems to be hung

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