Taxonomy fetching not working

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Taxonomy fetching not working

Deepthi Thomas Kannanayakal
Hi Galaxy team,

I am having problems with taxonomy information fetching.(Metagenomic Analysses->Fetch taxonomic representation).

According to the following link

http://dev.list.galaxyproject.org/quot-Fetch-taxonomic-representation-quot-DOESN-T-WORK-td4565489.html

I have installed libraries from https://bitbucket.org/natefoo/taxonomy
I have installed them in my local directory(not in /usr/local).  But I am still having problem
/bin/sh: taxBuilder: command not found

What am I missing here?

Thanks,
Deeps
Deepthi Theresa Thomas Kannanayakal

Bioinformatics Database Specialist
Sun Visual Genomic Centre, 
Suite 1150,  Health Science Centre
3330 Hospital Drive NW
Department of Biochemistry and Molecular Biology
Faculty of Medicine,  University of Calgary
T2N 4N1
Calgary,  Alberta,  Canada


Ph: (403) - 210 6661   Fax: (403) - 210 9538

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Re: Taxonomy fetching not working

Adam Brenner
Deeps,
It does not appear that you have installed taxBuilder on your system. What commands did you use to compile it on your system?
If you type 'which taxBuilder' it should return no results (assuming installed incorrectly). You will need to 'make clean' then 'make all' then manually move the binary files it produces into some environmental $PATH.

Hope that helps,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]


On Fri, May 3, 2013 at 3:58 PM, Deepthi Thomas Kannanayakal <[hidden email]> wrote:
Hi Galaxy team,

I am having problems with taxonomy information fetching.(Metagenomic Analysses->Fetch taxonomic representation).

According to the following link

http://dev.list.galaxyproject.org/quot-Fetch-taxonomic-representation-quot-DOESN-T-WORK-td4565489.html

I have installed libraries from https://bitbucket.org/natefoo/taxonomy
I have installed them in my local directory(not in /usr/local).  But I am still having problem
/bin/sh: taxBuilder: command not found

What am I missing here?

Thanks,
Deeps
Deepthi Theresa Thomas Kannanayakal

Bioinformatics Database Specialist
Sun Visual Genomic Centre, 
Suite 1150,  Health Science Centre
3330 Hospital Drive NW
Department of Biochemistry and Molecular Biology
Faculty of Medicine,  University of Calgary
T2N 4N1
Calgary,  Alberta,  Canada


Ph: <a href="tel:%28403%29%20-%20210%206661" value="+14032106661" target="_blank">(403) - 210 6661   Fax: <a href="tel:%28403%29%20-%20210%209538" value="+14032109538" target="_blank">(403) - 210 9538

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/