Rdp classifier

[Munmun Sarkar]

Hi all
  I am very new to using qiime and this is my first post. Recently, I was trying to install qiime in my system. During running assign_taxonomy.py file, it was asking me to install rdp classifier. I got the version 2.11 but in most of the documentation version 2.2 is mentioned and I couldn't get the source of that version.

I have two queries

1. where can I get the version 2.2 or should I continue with 2.11 (there might be more bug in the newer version)
2. detail about how to install and set the path of the classifier.


Thank you
Munmun

[TonyWalters]

Hello,

I haven't tested newer versions of the RDP classifier. It might work in QIIME, so you can try it, but if not, here is the link to the 2.2 version and install notes:
http://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.2.zip/download
http://qiime.org/install/install.html#rdp-install

The different versions of the software sometimes have different parameter names and formats for the expected input/output files, hence the reason you are often restricted in the versions you can use within QIIME.

[Munmun Sarkar]

 Hello Tony
  Thank you for replying to my queries. I have tried setting the path to the classifier as per the documentation. However I am getting the following error

bash: export: `rdp_classifier_2.2/rdp_classifier-2.2.jar': not a valid identifier

 any suggestion what might be the reason. I had specified path for classifier 2.11 previously. Is there any conflict due to that reason. Please suggest me what to do.

Thank you
Munmun

[TonyWalters]

Hello,

It sounds like the absolute filepath isn't being specified for your rdp_classifier-2.2.jar file.

See: http://www.linuxquestions.org/questions/linux-general-1/absolute-and-relative-paths-256350/
Can you confirm the absolute filepath for that file? You will need to edit the .bashrc file to fix the export command to point to the full filepath. You may be able to open the .bashrc file in a text editor, but, depending upon your system, you might need to use the vim editor, e.g., open a terminal, type:

vim .bashrc
Here is a guide to using vim: https://www.linux.com/learn/vim-101-beginners-guide-vim
You will want to find the line that looks like this:
export RDP_JAR_PATH=rdp_classifier_2.2/rdp_classifier-2.2.jar
and fix the rdp_classifier_2.2/rdp_classifier-2.2.jar to reflect the absolute filepath.