📝 Update databases docs

📝 Fix typos in databases docs
🔥📝 Remove misleading note on autometa being packaged with markers
📝 Add code block template commands to download/format markers

Author: evanroyrees

docs/source/databases.rst

@@ -2,10 +2,31 @@
 Databases
 =========
 
+If you are running Autometa for the first time you will need to download and format a few databases.
+You may do this manually or using a few Autometa helper scripts. If you would like to use Autometa's
+scripts for this, you will first need to install Autometa (See :ref:`Installation`).
+
+The following sections use a pair of commands to configure autometa such that the database is updated
+according to its respective path.
+
 Markers
 #######
 
-Autometa comes packaged with the necessary markers files. Links to these markers files and their associated cutoff values are below:
+.. code-block:: bash
+    
+    # Point Autometa to where you would like your markers database directory
+    autometa-config \
+        --section databases --option markers \
+        --value <path/to/your/markers/database/directory>
+    
+    # Update your markers database directory
+    autometa-update-databases --update-markers
+
+.. alert::
+    
+    Do NOT use a trailing slash, e.g. NO ``/`` for the database directory paths!
+
+Links to these markers files and their associated cutoff values are below:
 
 - bacteria single-copy-markers - `link <https://raw.githubusercontent.com/KwanLab/Autometa/main/autometa/databases/markers/bacteria.single_copy.hmm>`__
 - bacteria single-copy-markers cutoffs - `link <https://raw.githubusercontent.com/KwanLab/Autometa/main/autometa/databases/markers/bacteria.single_copy.cutoffs>`__
@@ -15,10 +36,6 @@ Autometa comes packaged with the necessary markers files. Links to these markers
 NCBI
 ####
 
-If you are running Autometa for the first time you will need to download the NCBI databases.
-You may do this manually or using a few Autometa helper scripts. If you would like to use Autometa's
-scripts for this, you will first need to download Autometa (See :ref:`Installation`).
-
 .. code-block:: bash
 
     # First configure where you want to download the NCBI databases
@@ -31,7 +48,7 @@ scripts for this, you will first need to download Autometa (See :ref:`Installati
 
 .. note::
 
-    You can check the default config paths using ``autometa-config --print``.
+    You can check the config paths using ``autometa-config --print``.
 
     See ``autometa-update-databases -h`` and ``autometa-config -h`` for full list of options.
 
@@ -41,7 +58,7 @@ The previous command will download the following NCBI databases:
     - `ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz <https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz>`_
 - prot.accession2taxid.gz
     - `ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz <https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz>`_
-- nodes.dmp, names.dmp and merged.dmp - Found within
+- nodes.dmp, names.dmp, merged.dmp and delnodes.dmp - Found within
     - `ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz <ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz>`_
 
 After these files are downloaded, the ``taxdump.tar.gz`` tarball's files are extracted and the non-redundant protein database (``nr.gz``)
@@ -50,11 +67,8 @@ is formatted as a diamond database (i.e. ``nr.dmnd``). This will significantly s
 Genome Taxonomy Database (GTDB)
 ###############################
 
-If you would like to incorporate the benefits of using the Genome Taxonomy Database.
-You may do this manually or using a few Autometa helper scripts. If you would like to use Autometa's
-scripts for this, you will first need to install Autometa (See :ref:`Installation`).
-
-You can either run the following script or manually download the respective databases.
+If you would like to incorporate the benefits of using the Genome Taxonomy Database,
+you can either run the following script or manually download the respective databases.
 
 .. code-block:: bash
 
@@ -87,16 +101,20 @@ The previous command will download the following GTDB databases and format the `
     - `gtdb-taxdump.tar.gz <https://github.com/shenwei356/gtdb-taxdump/releases/latest/download/gtdb-taxdump.tar.gz>`_
 
 
-Once unzipped `gtdb-taxdump.tar.gz` will have the taxdump files of all the respective GTDB releases. Make sure that the release you use is in line with the `gtdb_proteins_aa_reps.tar.gz` release version. It's better to always use the latest version. 
+Once unzipped `gtdb-taxdump.tar.gz` will have the taxdump files of all the respective GTDB releases. 
+Make sure that the release you use is in line with the `gtdb_proteins_aa_reps.tar.gz` release version. 
+It's better to always use the latest version. 
 
-All the taxonomy files for a specific taxonomy database should be in a single directory. You can now copy the taxdump files of the desired release version in the sample directory as `gtdb.dmnd`
+All the taxonomy files for a specific taxonomy database should be in a single directory. 
+You can now copy the taxdump files of the desired release version in the sample directory as `gtdb.dmnd`
 
-Alternatively if you have manually downloaded `gtdb_proteins_aa_reps.tar.gz` and `gtdb-taxdump.tar.gz` you can run the following command to format the `gtdb_proteins_aa_reps.tar.gz` to generate `gtdb.dmnd` and make it ready for Autometa.
+Alternatively if you have manually downloaded `gtdb_proteins_aa_reps.tar.gz` and `gtdb-taxdump.tar.gz` you can run the 
+following command to format the `gtdb_proteins_aa_reps.tar.gz` to generate `gtdb.dmnd` and make it ready for Autometa.
 
 .. code-block:: bash
 
-    python -m autometa.taxonomy.gtdb --reps-faa <path/to/gtdb_proteins_aa_reps.tar.gz> --dbdir <path/to/output_directory> --cpus 20
+    autometa-setup-gtdb --reps-faa <path/to/gtdb_proteins_aa_reps.tar.gz> --dbdir <path/to/output_directory> --cpus 20
 
 .. note::
 
-    Again Make sure that the formatted `gtdb_proteins_aa_reps.tar.gz` databse and gtdb taxdump files are in the same directory. 
+    Again Make sure that the formatted `gtdb_proteins_aa_reps.tar.gz` database and gtdb taxdump files are in the same directory.