Answers.Body: <p>The benefit of using the conda package is that you no longer need to know or care exactly where the jar files are (that many java-based packages require this is TERRIBLE design). The example <code>java -jar ...</code> command in your post becomes:</p>
  
  <pre><code>Clustering derep -m '#=GC_RF' -o derep.fa all_seqs.ids all_seqs.samples alignment/*.fasta
  </code></pre>
  
  <p>in the bioconda version. In bioconda packages, there are wrapper (usually python) scripts meant to provide somewhat friendlier interfaces to java programs that otherwise lack executables. In this case, RDP Classfier has the following executables in bioconda:</p>
  
  <ul>
  <li>AbundanceStats</li>
  <li>AlignmentTools</li>
  <li>Clustering</li>
  <li>FrameBot</li>
  <li>KmerFilter</li>
  <li>ProbeMatch</li>
  <li>ReadSeq</li>
  <li>SeqFilters</li>
  <li>SequenceMatch</li>
  <li>hmmgs</li>
  <li>classifier</li>
  </ul>
  
  <p>If you really want to know, the .jar file is under <code>$PREFIX/share/rdptools-$PKG_VERSION-$PKG_BUILDNUM/</code>, where <code>$PREFIX</code> is where ever the environment is and the other two variables indicate the package version and build number (at the moment, <code>rdptools-2.0.2-1</code> would be the likely folder name).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-16T19:18:35.707Z
Answers.LastActivityDate: 2019-11-16T19:18:35.707Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I am interested in using RDP classifier and RDPTools at the command line.  In following the docs from RDP, I ran into <a href="https://github.com/rdpstaff/RDPTools/issues/22" rel="nofollow noreferrer">this issue</a> during the build, after running <code>make</code>:</p>
  
  <pre><code>BUILD FAILED
  /home/denir/bin/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.
  
  Total time: 1 second
  Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
  make: *** [Clustering/dist/Clustering.jar] Error 1
  </code></pre>
  
  <p>As one user suggested, I have tried downgrading from ant 1.10 to ant 1.9, this didn't work for me.</p>
  
  <p>I would rather not downgrade to JDK 7 as another user suggested if possible so I am looking for alternatives. One user was able to install rdp classifier with bioconda. I was able to do that OK. However, I'm not sure where to go from here? The tutorial provided with commands like: </p>
  
  <pre><code>java -Xmx2g -jar ~/RDPTools/Clustering.jar derep -m '#=GC_RF' -o derep.fa all_seqs.ids all_seqs.samples alignment/*.fasta
  </code></pre>
  
  <p>Depend on the build created using the install method recommended by RDP.  </p>
  
  <p>Does anyone else use rdp classifier installed via conda?  Is there a quickstart guide out there that I could refer to?  Thanks so much for your help!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-16T18:00:33.927Z
Comments.Text: I'm not entirely clear on what the problem is. You seem to be saying that you have managed to install it OK through bioconda. What's wrong with that command you show? Is it that you don't know where bioconda installed the `Clustering.jar` file? Also, please [edit] your question and add your operating system. If you are on Linux, and the issue is that you don't know where the jar file is, try `sudo updatedb; locate Clustering.jar`.
Comments.UserDisplayName: terdon
Tags: <bioconda>
Title: How to Installing & Using RDP Classifier through bioconda?
ThreadText: # How to Installing & Using RDP Classifier through bioconda?
  
  (Asked by: username_0 on 2019-11-16)
  
  I am interested in using RDP classifier and RDPTools at the command line. In following the docs from RDP, I ran into [this issue](https://github.com/rdpstaff/RDPTools/issues/22) during the build, after running `make`:
  
  ```
  BUILD FAILED
  /home/denir/bin/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
  /home/denir/bin/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.
  
  Total time: 1 second
  Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
  make: *** [Clustering/dist/Clustering.jar] Error 1
  
  ```
  
  As one user suggested, I have tried downgrading from ant 1.10 to ant 1.9, this didn't work for me.
  
  I would rather not downgrade to JDK 7 as another user suggested if possible so I am looking for alternatives. One user was able to install rdp classifier with bioconda. I was able to do that OK. However, I'm not sure where to go from here? The tutorial provided with commands like:
  
  ```
  java -Xmx2g -jar ~/RDPTools/Clustering.jar derep -m '#=GC_RF' -o derep.fa all_seqs.ids all_seqs.samples alignment/*.fasta
  
  ```
  
  Depend on the build created using the install method recommended by RDP.
  
  Does anyone else use rdp classifier installed via conda? Is there a quickstart guide out there that I could refer to? Thanks so much for your help!
  
  **Tags:** bioconda
  
  > **Comments:**
  > **username_1**: I'm not entirely clear on what the problem is. You seem to be saying that you have managed to install it OK through bioconda. What's wrong with that command you show? Is it that you don't know where bioconda installed the `Clustering.jar` file? Also, please [edit] your question and add your operating system. If you are on Linux, and the issue is that you don't know where the jar file is, try `sudo updatedb; locate Clustering.jar`.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-11-16. Score: 1
  
  The benefit of using the conda package is that you no longer need to know or care exactly where the jar files are (that many java-based packages require this is TERRIBLE design). The example `java -jar ...` command in your post becomes:
  
  ```
  Clustering derep -m '#=GC_RF' -o derep.fa all_seqs.ids all_seqs.samples alignment/*.fasta
  
  ```
  
  in the bioconda version. In bioconda packages, there are wrapper (usually python) scripts meant to provide somewhat friendlier interfaces to java programs that otherwise lack executables. In this case, RDP Classfier has the following executables in bioconda:
  
  * AbundanceStats
  * AlignmentTools
  * Clustering
  * FrameBot
  * KmerFilter
  * ProbeMatch
  * ReadSeq
  * SeqFilters
  * SequenceMatch
  * hmmgs
  * classifier
  
  If you really want to know, the .jar file is under `$PREFIX/share/rdptools-$PKG_VERSION-$PKG_BUILDNUM/`, where `$PREFIX` is where ever the environment is and the other two variables indicate the package version and build number (at the moment, `rdptools-2.0.2-1` would be the likely folder name).
  
  
  ---
  
  