Answers.Body: <p>The <code>--config</code> file option for Manta can be used to override the defaults in the global config file. If you type <code>configManta.py -h</code>, you'll see where the global config file has been installed. For me, it's here:</p>
  <pre><code>/home/steve/miniconda3/envs/manta/share/manta-1.6.0-1/bin/configManta.py.ini
  </code></pre>
  <p>So the command in your log file takes a specific config file installed into:</p>
  <pre><code>/opt/illumina/Isis/2.6.25.18/...
  </code></pre>
  <p>I suspect 'Isis' is a reference to Illumina's analysis tool 'IsisRNA'. Papers that mention Illumina's 'RnaReadCounter' tool, say that it is part of the <em>internal</em> analysis tool 'IsisRNA'. Because it's one of Illumina's in-house tools, I think you'd need to contact Illumina support to get a copy. I would only do this though if you need to reproduce <em>exactly</em> as per the command in your log file. If you only need to roughly reproduce the output, the defaults in the global config file are probably fine.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-04-08T23:45:09.043Z
Answers.LastActivityDate: 2021-04-08T23:45:09.043Z
Answers.UserDisplayName: Steve
Body: <p>I trying to locally reproduce a <a href="https://github.com/Illumina/manta" rel="nofollow noreferrer">Manta</a> run as seen in the <em>log</em> of an illumina basespace <a href="https://emea.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/rna-seq-alignment.html" rel="nofollow noreferrer">RNA-Seq Alignment tool v1.1.1</a> run I've done. The log reads as follows:</p>
  <pre><code>[LOG][2021-03-12 20:58:56.377]03/12/2021,20:58:56.193,Launch process:  \
  /path_to_RNA_Tools/bin/python  \
  '/path_to_RNA_Tools/Manta/bin/configManta.py'  \
  --rna --normalBam='path_to_alignments/alignments.bam' \
  --runDir='path_to_samples/CTR/replicates/CTR/MantaFusions/manta.run'  \
  --referenceFasta='/path_to_genomes/genome.fa' \
  --config '/opt/illumina/Isis/2.6.25.18/Workflows/WholeGenomeRnaSeqWorker/scripts/configManta.py.ini'
  </code></pre>
  <p>The file shown in the line above <code>configManta.py.ini</code> is however no were to be found.
  The <a href="https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md#advanced-configuration-options" rel="nofollow noreferrer">Manta user guide</a> states in the linked section</p>
  <blockquote>
  <p>Options listed in the file: <code>${MANTA_INSTALL_PATH}/bin/configManta.py.ini</code></p>
  </blockquote>
  <p>The <code>configManta.py</code> is in the expected directory, only the <code>configManta.py.ini</code> is absent.</p>
  <p>I am using <a href="https://anaconda.org/bioconda/manta" rel="nofollow noreferrer">Manta version  1.6.0 from bioconda</a>.</p>
  <p>Your insights will be much appreciated!</p>
  
Tags: <fusions>
Title: Manta SV caller: I can't find a file in the path specified by the user guide
ThreadText: # Manta SV caller: I can't find a file in the path specified by the user guide
  
  (Asked by: username_0 on 2021-04-08)
  
  I trying to locally reproduce a [Manta](https://github.com/Illumina/manta) run as seen in the *log* of an illumina basespace [RNA-Seq Alignment tool v1.1.1](https://emea.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/rna-seq-alignment.html) run I've done. The log reads as follows:
  
  ```
  [LOG][2021-03-12 20:58:56.377]03/12/2021,20:58:56.193,Launch process:  \
  /path_to_RNA_Tools/bin/python  \
  '/path_to_RNA_Tools/Manta/bin/configManta.py'  \
  --rna --normalBam='path_to_alignments/alignments.bam' \
  --runDir='path_to_samples/CTR/replicates/CTR/MantaFusions/manta.run'  \
  --referenceFasta='/path_to_genomes/genome.fa' \
  --config '/opt/illumina/Isis/2.6.25.18/Workflows/WholeGenomeRnaSeqWorker/scripts/configManta.py.ini'
  
  ```
  
  The file shown in the line above `configManta.py.ini` is however no were to be found.
  The [Manta user guide](https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md#advanced-configuration-options) states in the linked section
  
  > Options listed in the file: `${MANTA_INSTALL_PATH}/bin/configManta.py.ini`
  
  The `configManta.py` is in the expected directory, only the `configManta.py.ini` is absent.
  
  I am using [Manta version 1.6.0 from bioconda](https://anaconda.org/bioconda/manta).
  
  Your insights will be much appreciated!
  
  **Tags:** fusions
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-04-08. Score: 2 | Accepted answer
  
  The `--config` file option for Manta can be used to override the defaults in the global config file. If you type `configManta.py -h`, you'll see where the global config file has been installed. For me, it's here:
  
  ```
  /home/username_1/miniconda3/envs/manta/share/manta-1.6.0-1/bin/configManta.py.ini
  
  ```
  
  So the command in your log file takes a specific config file installed into:
  
  ```
  /opt/illumina/Isis/2.6.25.18/...
  
  ```
  
  I suspect 'Isis' is a reference to Illumina's analysis tool 'IsisRNA'. Papers that mention Illumina's 'RnaReadCounter' tool, say that it is part of the *internal* analysis tool 'IsisRNA'. Because it's one of Illumina's in-house tools, I think you'd need to contact Illumina support to get a copy. I would only do this though if you need to reproduce *exactly* as per the command in your log file. If you only need to roughly reproduce the output, the defaults in the global config file are probably fine.
  
  
  ---
  
  