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Question: Installing an old tool via a folder
0
gravatar for mccoykg
3.1 years ago by
mccoykg • 80
United States
mccoykg • 80 wrote:

Hi all! I'm having trouble installing an older version of a tool. The tool in question is the fastx_barcode_splitter_enhanced tool version 1.0.0. I can't install the old version directly though the tool shed but was able to download a folder with the old version, called b7b3d008e2d3. I've put that into the same location the new version's folder is in - /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/fastx_barcode_splitter_enhanced - and coded that into the shed_tool_conf.xml file as follows:

<section id="filter" name="Filter and Sort" version="">
  <tool file="toolshed.g2.bx.psu.edu/repos/lparsons/fastx_barcode_splitter_enhanced/b7b3d008e2d3/fastx_barcode_splitter_enhanced/fastx_barcode_splitter.xml" guid="toolshed.g2.bx.psu.edu/repos/lparsons/fastx_barcode_splitter_enhanced/cshl_princeton_fastx_barcode_splitter/1.0.0">
      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>fastx_barcode_splitter_enhanced</repository_name>
        <repository_owner>lparsons</repository_owner>
        <installed_changeset_revision>b7b3d008e2d3</installed_changeset_revision>
        <id>toolshed.g2.bx.psu.edu/repos/lparsons/fastx_barcode_splitter_enhanced/cshl_princeton_fastx_barcode_splitter/1.0.0</id>
        <version>1.0.0</version>
    </tool>
</section>

However, the tool still isn't showing up. Is there another step I'm missing? Unless the code above is wrong, I'm sure there's some connection I've missed, but I can't figure out what that might be.

Thanks much,

K
tool installation • 801 views
ADD COMMENT • link •
modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by mccoykg • 80
1
gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The 1.0.0 version of the tool is still in both the Main Tool Shed and the Test Tool Shed. Installing from one of these locations will probably solve the problem (Test might be easier because of the UI changes made to Main). Multiple versions of tools in the tool panel are supported (if you need both).

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

I'm sorry, but I just can't seem to get it - is it possible that you can see the old version because you're an admin and I can't? Here are some screenshots of what I see when I search for the tool: as you can see there is only one installable revision of fastx_barcode_splitter_enhanced listed, and it is the 1.1 version.

http://pasteboard.co/25yakMWE.png

http://pasteboard.co/25yjGDV4.png

If I'm missing it, could you step me through which specific buttons to click to get to the old version and install it? It's very possible I'm missing something obvious.

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by mccoykg • 80

Searching the Main Tool Shed, not logged in at all, both tool version are present. You want the older devteam repository for version 1.0.0 (not named with "enhanced"). See these pics for help http://imgur.com/a/vzJHf. Also, this is the direct link to the repo: https://toolshed.g2.bx.psu.edu/view/devteam/fastx_barcode_splitter/8abdedf55101

Be sure to clear out anything else you added from the manual install before loading from the tool shed or install problems are almost a certainty.

Let us know if it works! Jen

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Oh! I'm sorry, I think you misunderstood my question. I'm trying to install an older version of the enhanced fastx_barcode_splitter, because the latest version isn't running on my local instance, but the second-latest version ran fine. I'm not trying to install the devteam version at all. I've been told by the owner of the enhanced fastx_barcode_splitter that an older version of his tool is available to install on the main toolshed, but I can't seem to find that.

In my original question, the folder I'm trying to link in the shed_tool_conf.xml file is the second-latest version of fastx_barcode_splitter, which I still have a folder of from my local test instance of galaxy. If the old version of enhanced fastx_barcode_splitter is not actually available I could just use this folder, but I can't get it to connect to Galaxy properly - even adding the path to the tool doesn't make it show up.

So basically I need to either install an older version of the enhanced fastx_barcode_splitter from the toolshed (the easiest option if it actually is available) or stick this folder in to the right place and connect everything up myself (something I'm currently trying to do but somehow failing at).

EDIT: I actually don't have the 1.0.0 version, I have the 1.1 version labeled as 1.0.0 for some reason, so this question isn't meaningful any more. I've contacted the repository owner to try to get the old version. Thanks for your help.

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by mccoykg • 80
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