Question: Using rdp_classifier via qiime in Galaxy
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2.4 years ago by
5911468930
5911468930 wrote:

Dear friends,

I just want to use RDP classifier in Galaxy via the python script, assign_taxonomy.py, which was from QIIME in a server. Now the question is that when I ran the python code in Galaxy, there is always a error for rdp classifier:

"assign_taxonomy.py: error: RDP classifier is not installed or not accessible to QIIME. See install instructions here: http://qiime.org/install/install.html#rdp-install"

But I am surely that the variable RDP_JAR_PATH has been verified. Because when I run "export $RDP_JAR_PATH" in the server, it says that /galaxy-dist/tools/rdp_classifier_2.5/rdp_classifier-2.5.jar. And if I run the python code in the command line of the server, I will get the right output of rdp classifier and no recorded error.

So what should I do with the Galaxy to make the python code to recognize the variable of RDP_JAR_PATH. Thanks a lot!

Kai


software error galaxy • 805 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by 5911468930
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gravatar for 591146893
2.4 years ago by
5911468930
5911468930 wrote:

Actually, I solved it by myself. I followed the QIIME configuration instruction about RDP classifier and reset the variables for RDP_JAR_PATH. Then the Galaxy works.

ADD COMMENTlink written 2.4 years ago by 5911468930
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