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jourdrenjourdren
committedAug 18, 2016
UPDATE: Replace link to the old genomic platform websites by the new ones.
·
v3.1.1v2.0-rc17
1 parent 9faf2a6 commit d8efa89

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-23
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‎INSTALL.txt

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@@ -3,4 +3,4 @@ INSTALLING Aozan
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To install Aozan, see the documentation on our website :
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http://transcriptome.ens.fr/aozan
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http://outils.genomique.biologie.ens.fr/aozan

‎src/main/java/files/template_index_run.html

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</div>
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<!--END_SECTION-->
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</div>
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<div class="footer">Generated by <a href="http://transcriptome.ens.fr/aozan">Aozan </a>(version ${VERSION})</div>
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<div class="footer">Generated by <a href="${WEBSITE}">${APP_NAME} </a>(version ${VERSION})</div>
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</body>
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</html>

‎src/main/python/common.py

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@@ -727,12 +727,10 @@ def create_html_index_file(conf, run_id, sections):
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write_lines = True
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elif write_lines is True:
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if '${RUN_ID}' in line:
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result += line.replace('${RUN_ID}', run_id) + '\n'
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elif '${VERSION}' in line:
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result += line.replace('${VERSION}', Globals.APP_VERSION_STRING) + '\n'
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else:
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result += line + '\n'
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result += line.replace('${RUN_ID}', run_id). \
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replace('${APP_NAME}', Globals.APP_NAME). \
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replace('${VERSION}', Globals.APP_VERSION_STRING). \
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replace('${WEBSITE}', Globals.WEBSITE_URL) + '\n'
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f_out = open(output_file_path, 'w')
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f_out.write(result)

‎src/site/resources/quality_control_example_project/2013_0001_ATCACG_L001_R1_001-fastqscreen.html

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@@ -211,7 +211,7 @@ <h2 style="text-align:center">Data simulated</h2>
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</p>
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<p>&nbsp;</p>
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</div>
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<div class="footer"> Site <a href="http://transcriptome.ens.fr/aozan">Aozan</a>
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<div class="footer"> Site <a href="@@@WEBSITE@@@">@@@APPNAME@@@</a>
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(version 1.2) </div>
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</body>
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</html>

‎src/site/resources/quality_control_example_project/Project_name_1-fastqscreen.html

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</div>
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<div class="footer">
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Generated by
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<a href="http://transcriptome.ens.fr/aozan">Aozan</a>
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<a href="@@@WEBSITE@@@">@@@APPNAME@@@</a>
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(version 1.4)
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</div>

‎src/site/resources/quality_control_example_project/lane1-potentialindices.html

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<div class="footer">
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<span>
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Generated by
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<a href="http://transcriptome.ens.fr/aozan">
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Aozan
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<a href="@@@WEBSITE@@@">
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@@@APPNAME@@@
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</a>
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(version 1.3
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)

‎src/site/resources/quality_control_example_project/lane2_Undetermined_L002_R1_001-potentialindices.html

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<p>_</p>
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</div>
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<div class="footer">
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<span> Generated by <a href="http://transcriptome.ens.fr/aozan">
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Aozan </a> (version 1.3 )
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<span> Generated by <a href="@@@WEBSITE@@@">
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@@@APPNAME@@@ </a> (version 1.3 )
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</span>
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</div>
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</body>
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</html>
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</html>

‎src/site/resources/quality_control_example_report.html

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@@ -1074,7 +1074,7 @@ <h3>Read 1</h3>
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</table>
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<p>&nbsp;</p>
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</div>
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<div class="footer"> Generated by <a href="http://transcriptome.ens.fr/aozan">Aozan</a>
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<div class="footer"> Generated by <a href="@@@WEBSITE@@@">@@@APPNAME@@@</a>
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(version 1.4) </div>
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</body>
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</html>

‎src/site/site.xml

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<bannerLeft>
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<name>ENS</name>
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<src>images/logo_genomicpariscentre-90pxh.png</src>
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<href>http://transcriptome.ens.fr/sgdb</href>
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<href>https://www.genomique.biologie.ens.fr/</href>
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</bannerLeft>
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<bannerRight>
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<name>Aozan</name>
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<body>
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<links>
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<item name="Genomic Paris Centre"
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href="http://transcriptome.ens.fr" />
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href="https://www.genomique.biologie.ens.fr" />
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<item name="École normale supérieure"
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href="http://www.ens.fr" />
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</links>

‎src/site/xdoc/installing.xml

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<ul>
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<li><a href="download.html">Download Aozan</a> on our website.</li>
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<source>$ wget http://transcriptome.ens.fr/aozan/aozan-@@@VERSION@@@.tar.gz</source>
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<source>$ wget @@@WEBSITE@@@/aozan-@@@VERSION@@@.tar.gz</source>
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<li>Unzip the archive where you want install the software.</li>
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‎src/site/xdoc/qc-samples-tests.xml

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<p>To avoid too long computation, the mapping on genomes is limited to a small set of the reads of the FASTQ files.
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By default 200,000 reads PF (passing illumina filters) are used for each sample (It's enough for estimate the contamination in a sample).</p>
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<p>Aozan reuses <a href="http://transcriptome.ens.fr/eoulsan" target="_blank">Eoulsan</a> to handle alignments and
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especially the <a href="http://transcriptome.ens.fr/eoulsan/datarepositories.html" target="_blank">repository system for genomes and genomes indexes</a>.</p>
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<p>Aozan reuses <a href="http://outils.genomique.biologie.ens.fr/eoulsan" target="_blank">Eoulsan</a> to handle alignments and
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especially the <a href="http://outils.genomique.biologie.ens.fr/eoulsan/datarepositories.html" target="_blank">repository system for genomes and genomes indexes</a>.</p>
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<p>If no FastQ Screen test property is set, FastQ Screen will not be launch on FASTQ data.</p>
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‎src/site/xdoc/quickstart.xml

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Executing these tasks after each sequencing process is a laborious job. Aozan allows to
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save time by automate all these tasks. In addition, Aozan provide a Bcl2fastq CSV samplesheet generator
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from an XLS file to avoid common syntax errors in the CSV file and to allow usage of alias for the index
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sequences. This tool is available <a href="http://transcriptome.ens.fr/designvalidator">here</a>.
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sequences. This tool is available <a href="http://outils.genomique.biologie.ens.fr/samplesheetvalidator/">here</a>.
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</p>
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</section>
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‎src/site/xdoc/writingplugin.xml

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-DgroupId=com.example \
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-DartifactId=myaozanplugin \
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-Dversion=0.1-alpha-1 \
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-Durl=http://transcriptome.ens.fr/aozanplugin \
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-Durl=http://example.com/aozanplugin \
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-DinteractiveMode=false
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</source>
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