Professor of Cell sand Developmental Biology at Vanderbilt University

Question: Professor of Cell sand Developmental Biology at Vanderbilt University

3.3 years ago by

chin.chiang • 0

chin.chiang • 0 wrote:

Is there anyway to get access to Galaxy 1.5? I am currently limited to use Tophat version 0.9.

galaxy • 902 views

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modified 3.3 years ago by Martin Čech ♦♦ 4.9k • written 3.3 years ago by chin.chiang • 0

What is Galaxy 1.5? Galaxy does not have any version number (yet). You can refer to Galaxy by releases ... for example 15.05 or the upcoming 15.07 ...

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

3.3 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

you can update TopHat independently of your Galaxy version. If you are Admin, please go to the admin panel and upgrade your TopHat installation.

Also keep in mind that if you are referring to this (Galaxy Tool Version 0.9) version. Than your version is the latest version available. The Galaxy Tool version does not reflect the underlying TopHat version. Please click on the button next to the Galaxy tool version to see the underlying TopHat dependency.

Cheers,

Bjoern

ADD COMMENT • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

I am using usegalaxy web interface. Could you please give me instruction as how to load tophat2 into Galaxy?

Thank you, Chin

Chin Chiang, Ph.D Professor, Cell and Developmental Biology Vanderbilt University PMB 407935 MRB3 Rm 4114 465 21st. Ave, S. Nashville, TN 37240-7935 Tel: 615-343-4922 email: chin.chiang@vanderbilt.edu

From: Bjoern Gruening on Galaxy Biostar <notifications@biostars.org<mailto:notifications@biostars.org>> Reply-To: "galaxystar+36341863+code@biostars.io<mailto:galaxystar+36341863+code@biostars.io>" <galaxystar+36341863+code@biostars.io<mailto:galaxystar+36341863+code@biostars.io>> Date: Monday, August 3, 2015 at 3:25 AM To: Chin Chiang <chin.chiang@vanderbilt.edu<mailto:chin.chiang@vanderbilt.edu>> Subject: [galaxy-biostar] A: Professor of Cell sand Developmental Biology at Vanderbilt University

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Bjoern Gruening<http: biostar.usegalaxy.org="" u="" 1225=""/> wrote Answer: Professor of Cell sand Developmental Biology at Vanderbilt University<http: biostar.usegalaxy.org="" p="" 13565="" #13572="">:

Hi,

you can update TopHat independently of your Galaxy version. If you are Admin, please go to the admin panel and upgrade your TopHat installation.

Also keep in mind that if you are referring to this (Galaxy Tool Version 0.9) version. Than your version is the latest version available. The Galaxy Tool version does not reflect the underlying TopHat version. Please click on the button next to the Galaxy tool version to see the underlying TopHat dependency.

Cheers,

Bjoern

ADD REPLY • link written 3.3 years ago by chin.chiang • 0

Do you have an admin account? If so please follow this wiki entry: https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

3.3 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

I believe this is a misunderstanding of Galaxy Tool versioning.

The latest Tophat on usegalaxy.org is version 2.0.14. The version 0.9 is a version of Galaxy Tool...not the underlying Tophat software. You can see this details if you click on options/requirements

ADD COMMENT • link written 3.3 years ago by Martin Čech ♦♦ 4.9k

Yes, you are right. I have another question. When I ran cufflink using mouse genome reference annotation ( ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm10/Mus_musculus_UCSC_mm10.tar) I got nothing. Is this the right reference library to use?

Thanks, Chin On Aug 5, 2015, at 9:52 AM, Martin Čech on Galaxy Biostar <notifications@biostars.org<mailto:notifications@biostars.org>> wrote:

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org=""/>

User Martin Čech<http: biostar.usegalaxy.org="" u="" 1313=""/> wrote Answer: Professor of Cell sand Developmental Biology at Vanderbilt University<http: biostar.usegalaxy.org="" p="" 13565="" #13616="">:

I believe this is a misunderstanding of Galaxy Tool versioning.

The latest Tophat on usegalaxy.org<http: usegalaxy.org=""> is version 2.0.14. The version 0.9 is a version of Galaxy Tool...not the underlying Tophat software. You can see this details if you click on options/requirements

[http://i59.tinypic.com/1037dhd.png]

ADD REPLY • link written 3.3 years ago by chin.chiang • 0

Hello,

If the target reference genome is mm10 while mapping, then this is the correct source for reference annotation.

Data compressed in .tar format will only load the first file of the archive when using "Upload" into Galaxy. Instead, uncompress the data locally, then only upload the "genes.gtf" reference annotation for use with this tool suite. There are other reference files in this .tar bundle, and you can load those as well if wanted, but these are not used by the tools.

Thanks! Jen, Galaxy team

ADD REPLY • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

Next time please open a new question to help us keep the site clean,easy to navigate and search. Thanks.

ADD REPLY • link written 3.3 years ago by Martin Čech ♦♦ 4.9k

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