Question: using the galaxy for chip seq
gravatar for xuqi2016hangzhou
4.4 years ago by
European Union
xuqi2016hangzhou0 wrote:



I am a new user in galaxy. i have some problems now. I found that the system I using have the 1.0.1 version of macs and also have no CEAS, but when i watch the tutorial on youtube, it showed that galaxy have the macs 1,4,2 and also have CEAS. Do i need to install myself? Thanks!


all the best!


chip-seq • 1.1k views
ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by xuqi2016hangzhou0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The 1.0.1 tool wrapper version of MACS is associated with the tool application version of 

The repository in the Tool Shed is here, and can be added to a local or cloud Galaxy:

Other repositories for MACS exist in the Tool Shed not owned by "devteam" (the primary Galaxy team), including one that wraps the tool application version 1.4 (states "1.4.1" as a dependency, whether this functions on 1.4.2 is not noted, but the tool author can be asked). I do not believe that CEAS is available as a wrapped package, but this can be investigated, as explained next.

The MACS tool application version of 1.4.2 and CEAS is run on a Public Galaxy. Specifically, I am guessing you are working at the Cistrome Galaxy or that is where the tutorial you watched was sourced from. You could work there if not already. Or contact them through their google group to determine if/how it is possible to mirror their tool configuration on a local or cloud Galaxy.

From here you can decide how to proceed. Below I am including some notes about versions to help, if you or other readers are interested in more clarification about how versions are assigned.

Take care! Jen, Galaxy team


Versions and Tool Organization

General organization tips for tool nomenclature. Each component of a tool has a version. These can be layered and bundled.

First, tools will often have two associated version numbers (at least) that are important to know about for execution/reproducibility.

  • a version for the "tool wrapper" - this is the code that links a tool into the Galaxy framework.
  • a version for the underlying "tool application" or applications utilized by the wrapper -this is the actual tool (or tools) doing the analysis. These are assigned by tool authors. This version is noted when wrapped and included in Galaxy because most often the version of the wrapper and the version of the application are dependent on eachother (this is the case with MACS, and the dependency R used by it, both 3rd party tools). Some of these will even be part of larger suite of tools, that will then have another 3rd party "release" version/date (not the case with MACS, but good to know for tools in suites such as GATK).

Second, there are versions associated with how these are packaged, distributed, and connected with Galaxy, that are important to know about when administering a local or cloud Galaxy:

  • a version for the Tool Shed "tool repository" - this is the primary tool itself - given when checked into the Tool Shed (Main at or other)
  • a version for each associated "tool package" (optional) - this defines dependencies, including other "tool repositories" and configuration files - also given when checked into the Tool Shed  (Main at or other)
  • a version for a primary "Galaxy Distribution" (optional) for when tools are still a part of the primary repository (tools that have not been migrated to the Tool Shed yet or are code that is not a candidate to ever be migrated). This is produced by the primary Galaxy team along with community contributors.
  • a version for a public "Galaxy Distribution" (optional) for alternate releases by other groups, done similar to the above. Each will have their own process (Galaxy is open source).


ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Jennifer Hillman Jackson25k

I'd also like to just quickly point out that we are also testing a version of MACS2 on our public test server. We hope to release it to our main public site soon, but in the meantime if you would like to try it out and provide feedback and error reports, it is available for use at, under the "NGS: MACS2 (Beta Test)" section.

ADD REPLYlink written 4.4 years ago by Daniel Blankenberg ♦♦ 1.7k
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