Yes, it is figured out when I downloaded the version of 1.1.2. I thought is no 
longer available.

Thank you so much!

Best,

Xiaofei
________________________________
From: Nate Coraor [n...@bx.psu.edu]
Sent: Friday, April 04, 2014 11:20 AM
To: Wang, Xiaofei
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] version of SAM-to-BAM (CloudMap)

Hi Xiaofei,

You should be able to install 1.1.3 by selecting revision 3 of sam_to_bam from 
the "Preview and install" page (Admin -> Search and browse tool sheds -> Galaxy 
main tool shed -> sam_to_bam -> Preview and install), and then clicking 
"Install to Galaxy."

[Inline image 1]

You can tell what version of the tool it'll install by looking at the "Valid 
tools" section of the "Contents of this repository" box.

--nate


On Thu, Apr 3, 2014 at 6:16 PM, Wang, Xiaofei 
<xfw...@ku.edu<mailto:xfw...@ku.edu>> wrote:
Dear there,

When I run CloudMap EMS Variant Density Mapping workflow (takes VCF of 
heterozygous and homozygous variants to subtract) (imported from uploaded file) 
on local Galaxy instance, I got this
[X]
, when I wanted to edit the workflow. Also, I got this
The following tools are beinge executed with a different version from what was 
available when this workflow was last saved because the previous version is no 
longer available for use on this galaxy instance. To upgrade your workflow and 
dismiss this message simply edit the workflow and re-save it to update the 
stored tool version.

  *   
toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2<http://toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2>:
 using version '1.1.2' instead of version '1.1.3' indicated in this workflow.
  *   ,when I wanted to run the workflow.

I know it is the problem with version of SAM-to-BAM. But, when I searched the 
Tool sheds > Search and browse tool sheds, there is only version 1.1.4 for 
SAM-to-BAM. When I tried to edit the workflow from Workflow > ...> Edit, I did 
not find where could I change the version of SAM-to-BAM. When I clicked on 
SAM-to-BAM on the Workflow Canvas, it showed the version is 1.1.3 for it.

Could you tell me which version do I need exactly, and how to figure out this?

Thanks a lot!

Best,

Xiaofei

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<<inline: sam_to_bam_3.png>>

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