Tophat version not available in toolshed

Question: Tophat version not available in toolshed

3.4 years ago by

United States

I have been using a nice workflow on usegalaxy.org server and we are now migrating to our own local server. However, the tool versions available in the toolshed appear to be a problem for replicating my workflow. In particular, tophat v0.9, which interacts appropriately with both cufflinks 2.2.1.0 and cuffnorm 2.2.1.0 for analyzing dataset collections doesn't seem to be available in the toolshed. Does anyone have any idea how to get this tool for our local server?

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9

Thanks!

tophat v0.9 • 705 views

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modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by brian.hermann • 40

3.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Browse the revisions for Tophat2 in the Tool Shed to find the correct version and install. It is the first version, dated 11/17/2014. Also directly linked here:
https://toolshed.g2.bx.psu.edu/view/devteam/tophat2/ae06af1118dc

To let you know, this is how I found it: I review the repository "tip files" in the Tool Shed (under the right upper menu "Repository Actions"), then opened the tool .xml file to confirm the wrapper version "0.9". You need to be logged into the Tool Shed to do this.

Hopefully this helps! Jen, Galaxy team

ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you Jen – that did the trick. Sorry for the naïve question - I really appreciate the quick and comprehensive reply!

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: Thursday, July 16, 2015 1:59 PM To: Brian Hermann Subject: [galaxy-biostar] A: Tophat version not available in toolshed

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

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: Tophat version not available in toolshed<http: biostar.usegalaxy.org="" p="" 13185="" #13188="">:

Hello,

Browse the revisions for Tophat2 in the Tool Shed to find the correct version and install. It is the first version, dated 11/17/2014. Also directly linked here: https://toolshed.g2.bx.psu.edu/view/devteam/tophat2/ae06af1118dc

Hopefully this helps! Jen, Galaxy team

ADD REPLY • link written 3.4 years ago by brian.hermann • 40

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