added construction page

docs/construction.md

@@ -0,0 +1,86 @@
+# PanMAN Construction
+
+Here, we will learn to build PanMAN from various input formats.
+
+**Step 0:** The Steps below require panmanUtils, if not done so far, refer to [installation guide](install.md) to install panmanUtils. To check if panmanUtils is properly installed or not, run the following command, and it should execute without error
+```bash
+# enter into the panman directory (assuming $PANMAN directs to the panman repository directory)
+cd $PANMAN_HOME
+```
+```bash
+cd $PANMAN_HOME/build
+./panmanUtils --help
+```
+### Building PanMAN from PanGraph
+
+**Step 1:** Check if `sars_20.json` and `sars_20.nwk` files exist in `test` directory. Otherwise, follow the instructions to download the dataset. Alternatively, users can provide custom PanGraph (JSON) and tree topology (Newick format) files to build a panman. 
+
+```bash
+cd $PANMAN_HOME/dataset
+TODO
+```
+
+**Step 2:** Run panmanUtils with the following command to build a panman from PanGraph:
+
+```bash
+cd $PANMAN_HOME/build
+./panmanUtils -P $PANMAN_HOME/test/sars_20.json -N $PANMAN_HOME/test/sars_20.nwk -O sars_20
+```
+The above command will run <i>panmanUtils</i> program and build `sars_20.panman` in `$PANMAN_HOME/build/panman` directory.
+
+### Building PanMAN from GFA
+
+**Step 1:** Check if `sars_20.gfa` and `sars_20.nwk` files exist in `test` directory. Otherwise, follow the instructions to download the dataset. Alternatively, users can provide custom GFA and tree topology (Newick format) files to build a panman. 
+
+```bash
+cd $PANMAN_HOME/dataset
+TODO
+```
+
+**Step 2:** Run panmanUtils with the following command to build a panman from GFA:
+
+```bash
+cd $PANMAN_HOME/build
+./panmanUtils -G $PANMAN_HOME/test/sars_20.gfa -N $PANMAN_HOME/test/sars_20.nwk -O sars_20
+```
+The above command will run <i>panmanUtils</i> program and build `sars_20.panman` in `$PANMAN_HOME/build/panman` directory.
+
+### Building PanMAN from MSA (FASTA format)
+
+**Step 1:** Check if `sars_20.msa` and `sars_20.nwk` files exist in `test` directory. Otherwise, follow the instructions to download the dataset. Alternatively, users can provide custom MSA (FASTA format) and tree topology (Newick format) files to build a panman. 
+
+```bash
+cd $PANMAN_HOME/dataset
+TODO
+```
+
+**Step 2:** Run panmanUtils with the following command to build a panman from GFA:
+
+```bash
+cd $PANMAN_HOME/build
+./panmanUtils -M $PANMAN_HOME/test/sars_20.msa -N $PANMAN_HOME/test/sars_20.nwk -O sars_20
+```
+The above command will run <i>panmanUtils</i> program and build `sars_20.panman` in `$PANMAN_HOME/build/panman` directory.
+
+### Building PanMAN from raw genome sequences
+We provide scripts to construct <i>panmanUtils</i> inputs (PanGraph/GFA/MSA and Newick) from raw sequences (FASTA format), followed by building a panman.
+
+!!!Note
+    This script uses the PanGraph tool, PGGB, MAFFT, and MashTree to build input PanGraph, GFA, MSA, and Tree topology files, respectively. MashTree is not equipped when using PanGraph as input since the PanGraph tool constructs the tree topology too. 
+
+**Step 1:** Check if the `sars_20.fa` file exists in `test` directory. Otherwise, follow the instructions to download the dataset. Alternatively, users can provide custom raw sequences (FASTA format) to build a panman. 
+
+```bash
+cd $PANMAN_HOME/dataset
+TODO
+```
+
+**Step 2:** Run the following command to construct a panman from raw sequences.
+
+```bash
+cd $PANMAN_HOME/scripts
+chmod +x build_panman.sh
+./build_panman.sh
+```
+!!!Note
+    The above script is particularly designed to be used in the docker container build from either the provided docker image or the DockerFile (instructions provided [here](install.md))

mkdocs.yml

@@ -82,7 +82,8 @@ use_directory_urls: false
 nav:
   - Home: index.md
   - Install: install.md
-  - Quick Start: quickstart.md
+  - Construction: construction.md
+  - Utils: utils.md
 
 extra_javascript:
   - javascripts/mathjax.js