Create DocumentacionLefse.rst

DocumentacionLefse.rst

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+. _installation:
+
+Installation and Compilation of lefse
+======================================
+
+This document describes the steps to install and compile lefse
+
+System Requirements
+-------------------
+
+- **Compiler:** python/3.12_miniconda-24.7.1
+- **Dependencies:**
+
+Downloading and Extracting the Source Code
+------------------------------------------
+
+To download and extract the lefse source code, run:
+
+.. code-block:: bash
+    mkdir lefse
+    git clone https://github.com/SegataLab/lefse.git
+
+    Before compilation, load the necessary modules:
+
+.. code-block:: bash
+    module load python/3.12_miniconda-24.7.1
+
+Compiling lefse
+----------------
+conda activate lefse
+
+# Running the LEfSe commands with -h gives the list of available options
+
+# lefse-format_input.py convert the input data matrix to the format for LEfSe.
+
+# lefse_run.py performs the actual statistica analysis
+#
+# Apply LEfSe on the formatted data producing the results (to be further processed
+# for visualization with the other modules). The option available
+# can be listed using the -h option
+
+# lefse_plot_res.py visualizes the output
+#
+# Plot the list of biomarkers with their effect size
+# Severak graphical options are available for personalizing the output
+
+# lefse_plot_cladogram.py visualizes the output on a hierarchical tree
+#
+# Plot the representation of the biomarkers on the hierarchical tree
+
+# lefse_plot_features.py visualizes the raw-data features
+#
+# The module for exporting the raw-data representation of the features.
+# With the default options we will obtain the images for all the features that are
+# detected as biomarkers