text: user10791: I trying to locally reproduce a Manta run as seen in the log of an illumina basespace RNA-Seq Alignment tool v1.1.1 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 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.
  Your insights will be much appreciated!
  
  user10775: 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/steve/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.
  
original_text: 10791: <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>
   10775: <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>
  