Commit 1ddae0f9 authored by Christian Arnold's avatar Christian Arnold

Documentation update

parent cdd2db3a
Copyright (c) 2017 Christian Arnold (carnold@embl.de) & Ivan Berest (berest@embl.de)
Permission is hereby granted, free of charge, to any person obtaining a copy of this software
and associated documentation files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or
substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
,carnold,carnold,30.11.2017 14:57,file:///home/carnold/.config/libreoffice/4;
\ No newline at end of file
,carnold,carnold,05.12.2017 13:54,file:///home/carnold/.config/libreoffice/4;
\ No newline at end of file
......@@ -6,27 +6,52 @@ Try it out now!
The following quick start briefly summarizes the necessary steps to use our pipeline:
1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread). We recommend installing them via conda, in which case the installation is as easy as
1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread).
.. note:: Note that they all require Python 3.
``conda install -c bioconda snakemake bedtools samtools subread``
We recommend installing them via conda, in which case the installation is as easy as
If conda is not yet installed, follow the `installation instructions <https://conda.io/docs/user-guide/install/index.html>`_. If you want to install the tools manually and outside of the conda framework, see the following instructions for each of the tools: `snakemake <http://snakemake.readthedocs.io/en/stable/getting_started/installation.html>`_, `samtools <http://www.htslib.org/download>`_, `bedtools <http://bedtools.readthedocs.io/en/latest/content/installation.html>`_, `Subread <http://subread.sourceforge.net>`_.
.. code-block:: Bash
conda install -c bioconda snakemake bedtools samtools subread
If conda is not yet installed, follow the `installation instructions <https://conda.io/docs/user-guide/install/index.html>`_. Installation is quick and easy.
.. note:: You do not need to uninstall other Python installations or packages in order to use conda. Even if you already have a system Python, another Python installation from a source such as the macOS Homebrew package manager and globally installed packages from pip such as pandas and NumPy, you do not need to uninstall, remove, or change any of them before using conda.
If you want to install the tools manually and outside of the conda framework, see the following instructions for each of the tools: `snakemake <http://snakemake.readthedocs.io/en/stable/getting_started/installation.html>`_, `samtools <http://www.htslib.org/download>`_, `bedtools <http://bedtools.readthedocs.io/en/latest/content/installation.html>`_, `Subread <http://subread.sourceforge.net>`_.
2. Clone the Git repository:
``git clone https://git.embl.de/grp-zaugg/diffTF``
.. code-block:: Bash
git clone https://git.embl.de/grp-zaugg/diffTF
3. To run the example analysis for 50 TF, simply perform the following steps:
* Change into the ``example/input`` directory within the Git repository
``cd diffTF/example/input``
.. code-block:: Bash
cd diffTF/example/input
* Download the data via the download script
``sh downloadAllData.sh``
.. code-block:: Bash
sh downloadAllData.sh
* To test if the setup is correct, start a dryrun via the first helper script
``sh startAnalysisDryRun.sh``
.. code-block:: Bash
sh startAnalysisDryRun.sh
* Once the dryrun is successful, start the analysis via the second helper script
``sh startAnalysis.sh``
.. code-block:: Bash
sh startAnalysis.sh
4. To run your own analysis, modify the files ``config.json`` and ``sampleData.ts``. See the instructions in the section `Run your own analysis`_ for more details.
5. If your analysis finished successfully, take a look into the ``FINAL_OUTPUT`` folder within your specified output directory, which contains the summary tables and visualization of your analysis. If you received an error, take a look in Section :ref:`docs-errors` to troubleshoot.
......@@ -70,3 +95,15 @@ A working ``R`` installation is needed and a number of packages from either CRAN
============================================================
Run your own analysis
============================================================
Running your own analysis is almost as easy as running the example analysis. Carefully read and follow the following steps and notes:
1. Copy the files ``config.json`` and ``startAnalysis.sh`` to a directory of your choice.
2. Modify the file ``config.json`` accordingly. For example, we strongly recommend running the analysis for all TF instead of just 50 as for the example analysis. For this, simply change the parameter “TFs” to “all”. See Section 4 (TODO) for details about the meaning of the parameters. Do not delete or rename any parameters or sections.
3. Create a tab-separated file that defines the input data, in analogy to the file ``sampleData.tsv`` from the example analysis, and refer to that in the file ``config.json`` (parameter ``summaryFile``)
4. Adapt the file ``startAnalysis.sh`` if necessary (the exact command line call to Snakemake and the various Snakemake-related parameters)
.. note::
- For Snakemake to run properly, the R folder with the scripts has to be in the same folder as the Snakefile.
- Since running the pipeline might be computationally demanding, make sure you have enough space left on your device. As a guideline, analysis with 8 samples need around 12 GB of disk space, while a large analysis with 84 samples needs around 45 GB. Also, adjust the number of available cores accordingly. The pipeline can be invoked in a highly parallelized manner, so the more cores are available, the better!
- The pipeline is written in Snakemake, so for a deeper understanding and troubleshooting errors, some knowledge of Snakemake is invaluable. The same holds true for running the pipeline in a cluster setting. We recommend using a proper cluster configuration file in addition. For guidance and user convenience, we provide different cluster configuration files for a small (up to 10-15 samples) and large (>15 samples) analysis. See the folder ``src/clusterConfigurationTemplates`` for examples. Note that the sample number guidelines above are very rough estimates only. See the `Snakemake documentation <http://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#cluster-configuration>`_ for details for how to use cluster configuration files.
This diff is collapsed.
......@@ -15,11 +15,6 @@ To get yourself oriented, check the menu on the left or search what you are look
This site is organized into the following three parts:
.. toctree::
:maxdepth: 2
:caption: Contents:
.. toctree::
:maxdepth: 2
:caption: Quick Start and Installation
......
......@@ -9,20 +9,27 @@ Help, contribute and contact
If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation. For method-related questions, contact Judith B. Zaugg (judith.zaugg@embl.de) or Ivan Berest (berest@embl.de). For technical questions, contact Christian Arnold (christian.arnold@embl.de).
If you have questions, doubts, ideas or problems, please use the Issue Tracker at https://git.embl.de/grp-zaugg/diffTF/issues. We will respond in a timely manner.
If you have questions, doubts, ideas or problems, please use the `Bitbucket Issue Tracker <https://bitbucket.org/chrarnold/diffTF>`_. We will respond in a timely manner.
Citation
================
============================
If you use this software, please cite the following reference:
Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Dindler Rassmussen, Kristian Helin & Judith B. Zaugg. Genome-wide quantification of differential transcription factor activity: diffTF. 2017. submitted.
Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Dindler Rassmussen, Kristian Helin & Judith B. Zaugg. *Genome-wide quantification of differential transcription factor activity: diffTF*. 2017. submitted.
Frequently asked questions
=============
Change log
==========================
============================
COMING SOON
License
============================
diffTF is licensed under the MIT License:
.. literalinclude:: ../LICENSE.md
:language: text
This diff is collapsed.
This diff is collapsed.
......@@ -100,7 +100,7 @@
<li class="toctree-l1"><a class="reference internal" href="chapter2.html">Workflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#input">Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#output">Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline">Working with the pipeline</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline-and-frequently-asked-questions">Working with the pipeline and frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#handling-errors">Handling errors</a></li>
</ul>
<p class="caption"><span class="caption-text">Project Information</span></p>
......@@ -108,7 +108,6 @@
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html">Biological motivation</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#help-contribute-and-contact">Help, contribute and contact</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#citation">Citation</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#frequently-asked-questions">Frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#change-log">Change log</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#license">License</a></li>
</ul>
......
......@@ -100,7 +100,7 @@
<li class="toctree-l1"><a class="reference internal" href="chapter2.html">Workflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#input">Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#output">Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline">Working with the pipeline</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline-and-frequently-asked-questions">Working with the pipeline and frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#handling-errors">Handling errors</a></li>
</ul>
<p class="caption"><span class="caption-text">Project Information</span></p>
......@@ -108,7 +108,6 @@
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html">Biological motivation</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#help-contribute-and-contact">Help, contribute and contact</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#citation">Citation</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#frequently-asked-questions">Frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#change-log">Change log</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#license">License</a></li>
</ul>
......@@ -180,8 +179,6 @@
<p>To get yourself oriented, check the menu on the left or search what you are looking for in the search field in the upper left corner.</p>
<p>This site is organized into the following three parts:</p>
<div class="toctree-wrapper compound">
</div>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Quick Start and Installation</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="chapter1.html">Try it out now!</a></li>
......@@ -198,10 +195,20 @@
<p class="caption"><span class="caption-text">Pipeline Details</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html">Workflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#input">Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#input">Input</a><ul>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#summary">Summary</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#general-configuration-file">General configuration file</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#input-metadata">Input metadata</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#output">Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline">Working with the pipeline</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#handling-errors">Handling errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline-and-frequently-asked-questions">Working with the pipeline and frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#handling-errors">Handling errors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#error-types">Error types</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#identify-the-cause">Identify the cause</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#fixing-the-error">Fixing the error</a></li>
</ul>
</li>
</ul>
</div>
<div class="toctree-wrapper compound">
......@@ -210,7 +217,6 @@
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html">Biological motivation</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#help-contribute-and-contact">Help, contribute and contact</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#citation">Citation</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#frequently-asked-questions">Frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#change-log">Change log</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#license">License</a></li>
</ul>
......
......@@ -100,7 +100,7 @@
<li class="toctree-l1"><a class="reference internal" href="chapter2.html">Workflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#input">Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#output">Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline">Working with the pipeline</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline-and-frequently-asked-questions">Working with the pipeline and frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#handling-errors">Handling errors</a></li>
</ul>
<p class="caption"><span class="caption-text">Project Information</span></p>
......@@ -108,7 +108,6 @@
<li class="toctree-l1 current"><a class="current reference internal" href="#">Biological motivation</a></li>
<li class="toctree-l1"><a class="reference internal" href="#help-contribute-and-contact">Help, contribute and contact</a></li>
<li class="toctree-l1"><a class="reference internal" href="#citation">Citation</a></li>
<li class="toctree-l1"><a class="reference internal" href="#frequently-asked-questions">Frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="#change-log">Change log</a></li>
<li class="toctree-l1"><a class="reference internal" href="#license">License</a></li>
</ul>
......@@ -181,21 +180,39 @@
<div class="section" id="help-contribute-and-contact">
<h1>Help, contribute and contact<a class="headerlink" href="#help-contribute-and-contact" title="Permalink to this headline"></a></h1>
<p>If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation. For method-related questions, contact Judith B. Zaugg (<a class="reference external" href="mailto:judith&#46;zaugg&#37;&#52;&#48;embl&#46;de">judith<span>&#46;</span>zaugg<span>&#64;</span>embl<span>&#46;</span>de</a>) or Ivan Berest (<a class="reference external" href="mailto:berest&#37;&#52;&#48;embl&#46;de">berest<span>&#64;</span>embl<span>&#46;</span>de</a>). For technical questions, contact Christian Arnold (<a class="reference external" href="mailto:christian&#46;arnold&#37;&#52;&#48;embl&#46;de">christian<span>&#46;</span>arnold<span>&#64;</span>embl<span>&#46;</span>de</a>).</p>
<p>If you have questions, doubts, ideas or problems, please use the Issue Tracker at <a class="reference external" href="https://git.embl.de/grp-zaugg/diffTF/issues">https://git.embl.de/grp-zaugg/diffTF/issues</a>. We will respond in a timely manner.</p>
<p>If you have questions, doubts, ideas or problems, please use the <a class="reference external" href="https://bitbucket.org/chrarnold/diffTF">Bitbucket Issue Tracker</a>. We will respond in a timely manner.</p>
</div>
<div class="section" id="citation">
<h1>Citation<a class="headerlink" href="#citation" title="Permalink to this headline"></a></h1>
<p>If you use this software, please cite the following reference:
Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Dindler Rassmussen, Kristian Helin &amp; Judith B. Zaugg. Genome-wide quantification of differential transcription factor activity: diffTF. 2017. submitted.</p>
</div>
<div class="section" id="frequently-asked-questions">
<h1>Frequently asked questions<a class="headerlink" href="#frequently-asked-questions" title="Permalink to this headline"></a></h1>
<p>If you use this software, please cite the following reference:</p>
<p>Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Dindler Rassmussen, Kristian Helin &amp; Judith B. Zaugg. <em>Genome-wide quantification of differential transcription factor activity: diffTF</em>. 2017. submitted.</p>
</div>
<div class="section" id="change-log">
<h1>Change log<a class="headerlink" href="#change-log" title="Permalink to this headline"></a></h1>
<p>COMING SOON</p>
</div>
<div class="section" id="license">
<h1>License<a class="headerlink" href="#license" title="Permalink to this headline"></a></h1>
<p>diffTF is licensed under the MIT License:</p>
<div class="highlight-text"><div class="highlight"><pre><span></span>Copyright (c) 2017 Christian Arnold (carnold@embl.de) &amp; Ivan Berest (berest@embl.de)
Permission is hereby granted, free of charge, to any person obtaining a copy of this software
and associated documentation files (the &quot;Software&quot;), to deal in the Software without
restriction, including without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or
substantial portions of the Software.
THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
</pre></div>
</div>
</div>
......
......@@ -99,7 +99,7 @@
<li class="toctree-l1"><a class="reference internal" href="chapter2.html">Workflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#input">Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#output">Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline">Working with the pipeline</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline-and-frequently-asked-questions">Working with the pipeline and frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#handling-errors">Handling errors</a></li>
</ul>
<p class="caption"><span class="caption-text">Project Information</span></p>
......@@ -107,7 +107,6 @@
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html">Biological motivation</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#help-contribute-and-contact">Help, contribute and contact</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#citation">Citation</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#frequently-asked-questions">Frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#change-log">Change log</a></li>
<li class="toctree-l1"><a class="reference internal" href="projectInfo.html#license">License</a></li>
</ul>
......
This diff is collapsed.
......@@ -6,27 +6,52 @@ Try it out now!
The following quick start briefly summarizes the necessary steps to use our pipeline:
1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread). We recommend installing them via conda, in which case the installation is as easy as
1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread).
.. note:: Note that all tools require Python 3.
``conda install -c bioconda snakemake bedtools samtools subread``
We recommend installing them via conda, in which case the installation is as easy as
If conda is not yet installed, follow the `installation instructions <https://conda.io/docs/user-guide/install/index.html>`_. If you want to install the tools manually and outside of the conda framework, see the following instructions for each of the tools: `snakemake <http://snakemake.readthedocs.io/en/stable/getting_started/installation.html>`_, `samtools <http://www.htslib.org/download>`_, `bedtools <http://bedtools.readthedocs.io/en/latest/content/installation.html>`_, `Subread <http://subread.sourceforge.net>`_.
.. code-block:: Bash
conda install -c bioconda snakemake bedtools samtools subread
If conda is not yet installed, follow the `installation instructions <https://conda.io/docs/user-guide/install/index.html>`_. Installation is quick and easy.
.. note:: You do not need to uninstall other Python installations or packages in order to use conda. Even if you already have a system Python, another Python installation from a source such as the macOS Homebrew package manager and globally installed packages from pip such as pandas and NumPy, you do not need to uninstall, remove, or change any of them before using conda.
If you want to install the tools manually and outside of the conda framework, see the following instructions for each of the tools: `snakemake <http://snakemake.readthedocs.io/en/stable/getting_started/installation.html>`_, `samtools <http://www.htslib.org/download>`_, `bedtools <http://bedtools.readthedocs.io/en/latest/content/installation.html>`_, `Subread <http://subread.sourceforge.net>`_.
2. Clone the Git repository:
``git clone https://git.embl.de/grp-zaugg/diffTF``
.. code-block:: Bash
git clone https://git.embl.de/grp-zaugg/diffTF
3. To run the example analysis for 50 TF, simply perform the following steps:
* Change into the ``example/input`` directory within the Git repository
``cd diffTF/example/input``
.. code-block:: Bash
cd diffTF/example/input
* Download the data via the download script
``sh downloadAllData.sh``
.. code-block:: Bash
sh downloadAllData.sh
* To test if the setup is correct, start a dryrun via the first helper script
``sh startAnalysisDryRun.sh``
.. code-block:: Bash
sh startAnalysisDryRun.sh
* Once the dryrun is successful, start the analysis via the second helper script
``sh startAnalysis.sh``
.. code-block:: Bash
sh startAnalysis.sh
4. To run your own analysis, modify the files ``config.json`` and ``sampleData.ts``. See the instructions in the section `Run your own analysis`_ for more details.
5. If your analysis finished successfully, take a look into the ``FINAL_OUTPUT`` folder within your specified output directory, which contains the summary tables and visualization of your analysis. If you received an error, take a look in Section :ref:`docs-errors` to troubleshoot.
......@@ -70,3 +95,15 @@ A working ``R`` installation is needed and a number of packages from either CRAN
============================================================
Run your own analysis
============================================================
Running your own analysis is almost as easy as running the example analysis. Carefully read and follow the following steps and notes:
1. Copy the files ``config.json`` and ``startAnalysis.sh`` to a directory of your choice.
2. Modify the file ``config.json`` accordingly. For example, we strongly recommend running the analysis for all TF instead of just 50 as for the example analysis. For this, simply change the parameter “TFs” to “all”. See Section 4 (TODO) for details about the meaning of the parameters. Do not delete or rename any parameters or sections.
3. Create a tab-separated file that defines the input data, in analogy to the file ``sampleData.tsv`` from the example analysis, and refer to that in the file ``config.json`` (parameter ``summaryFile``)
4. Adapt the file ``startAnalysis.sh`` if necessary (the exact command line call to Snakemake and the various Snakemake-related parameters)
.. note::
- For Snakemake to run properly, the R folder with the scripts has to be in the same folder as the Snakefile.
- Since running the pipeline might be computationally demanding, make sure you have enough space left on your device. As a guideline, analysis with 8 samples need around 12 GB of disk space, while a large analysis with 84 samples needs around 45 GB. Also, adjust the number of available cores accordingly. The pipeline can be invoked in a highly parallelized manner, so the more cores are available, the better!
- The pipeline is written in Snakemake, so for a deeper understanding and troubleshooting errors, some knowledge of Snakemake is invaluable. The same holds true for running the pipeline in a cluster setting. We recommend using a proper cluster configuration file in addition. For guidance and user convenience, we provide different cluster configuration files for a small (up to 10-15 samples) and large (>15 samples) analysis. See the folder ``src/clusterConfigurationTemplates`` for examples. Note that the sample number guidelines above are very rough estimates only. See the `Snakemake documentation <http://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#cluster-configuration>`_ for details for how to use cluster configuration files.
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This site is organized into the following three parts:
.. toctree::
:maxdepth: 2
:caption: Contents:
.. toctree::
:maxdepth: 2
:caption: Quick Start and Installation
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......@@ -9,20 +9,27 @@ Help, contribute and contact
If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation. For method-related questions, contact Judith B. Zaugg (judith.zaugg@embl.de) or Ivan Berest (berest@embl.de). For technical questions, contact Christian Arnold (christian.arnold@embl.de).
If you have questions, doubts, ideas or problems, please use the Issue Tracker at https://git.embl.de/grp-zaugg/diffTF/issues. We will respond in a timely manner.
If you have questions, doubts, ideas or problems, please use the `Bitbucket Issue Tracker <https://bitbucket.org/chrarnold/diffTF>`_. We will respond in a timely manner.
Citation
================
============================
If you use this software, please cite the following reference:
Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Dindler Rassmussen, Kristian Helin & Judith B. Zaugg. Genome-wide quantification of differential transcription factor activity: diffTF. 2017. submitted.
Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Dindler Rassmussen, Kristian Helin & Judith B. Zaugg. *Genome-wide quantification of differential transcription factor activity: diffTF*. 2017. submitted.
Frequently asked questions
=============
Change log
==========================
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COMING SOON
License
============================
diffTF is licensed under the MIT License:
.. literalinclude:: ../LICENSE.md
:language: text
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