--- 12年4月18日，周三, JIE CHEN <jiechenable1987@gmail.com> 写道：

发件人: JIE CHEN <jiechenable1987@gmail.com>
主题: Re: [galaxy-dev] "Fetch taxonomic representation" DOESN'T WORK
收件人: galaxy-dev@lists.bx.psu.edu
日期: 2012年4月18日,周三,上午5:36
On Tue, Apr 17, 2012 at 1:00 PM, JIE CHEN <jiechenable1987@gmail.com> wrote:
Thank you Nate. Your advise is very helpful to me. I installed the binaries like you said. Right now the binaries can be run successfully in the command line prompt. However i run into other problems :
Failed to open input file: /usr/local/projects/galaxy-dist/tool-data/taxonomy/names.dmp
What i have done:

1. downloaded the .tar.gz file from the link you told me

2. tar zxvf name.tar.gz

3. then i found the three executables which are: taxBuilder, taxonomy2tree and tree2PS-fast.

4. made symbolic link of these files to the /usr/local/bin

what else shall i do? Thanks.

Tyler

The file may not exist. To generate the dependent files, you can try the following steps (change the path to yours):

Go to /mnt/galaxyTools/galaxy-central/scripts/taxonomy

Run processTaxonomy.sh, which will generate the file gi_taxid_sorted.txt and other files.
Link those files to the directory /mnt/galaxyTools/galaxy-central/tool-data/taxonomy
mkdir /mnt/galaxyTools/galaxy-central/tool-data/taxonomy
ls|awk '{print "ln -s /mnt/galaxyIndices/AdditionalData/taxonomy/"$1" /mnt/galaxyTools/galaxy-central/tool-data/taxonomy/"$1}'|sh

Sorry, it should be:

ls|awk '{print "ln -s /mnt/galaxyTools/galaxy-central/scripts/taxonomy/"$1" /mnt/galaxyTools/galaxy-central/tool-data/taxonomy/"$1}'|sh

or you can copy the directory /mnt/galaxyTools/galaxy-central/scripts/taxonomy to /mnt/galaxyTools/galaxy-central/tool-data/taxonomy

zhengqiu cai

On Tue, Apr 17, 2012 at 10:36 AM, Nate Coraor <nate@bx.psu.edu> wrote:

On Apr 17, 2012, at 1:32 PM, JIE CHEN wrote:

> Dear all,
>
> I was trying to run the build-in function "Fetch taxonomic representation" on my local instance of Galaxy, however it doesn't work as I expect.
> The error message is:
> /bin/sh: taxBuilder: not found
>
>
> Anyone has seen this problem before? Please tell me what to do to solve this problem? A lot of thanks

Hi Tyler,

Some Galaxy tools depend on external binaries not included in the Galaxy distribution, and this is one of those tools. The full list and where to get the tools from can be found here:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies

This specific tool can be found at:

https://bitbucket.org/natefoo/taxonomy

--nate

>
> Tyler
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