Updated documentation

CHANGELOG.md

@@ -11,6 +11,8 @@
   make classification by default
 - Allow build options to pass through to subsequent invocations (e.g.,
   k-mer length for 16S DBs)
+- Removed env options for library downloads (no longer available from
+  same NCBI location)
 
 ### Fixed
 - Removed mention of --fastq-input from Manual

docs/MANUAL.html

@@ -176,8 +176,6 @@ <h1 id="custom-databases">Custom Databases</h1>
 <li><code>protozoa</code>: RefSeq complete protozoan genomes/proteins</li>
 <li><code>nr</code>: NCBI non-redundant protein database</li>
 <li><code>nt</code>: NCBI non-redundant nucleotide database</li>
-<li><code>env_nr</code>: NCBI non-redundant protein database with sequences from large environmental sequencing projects</li>
-<li><code>env_nt</code>: NCBI non-redundant nucleotide database with sequences from large environmental sequencing projects</li>
 <li><code>UniVec</code>: NCBI-supplied database of vector, adapter, linker, and primer sequences that may be contaminating sequencing projects and/or assemblies</li>
 <li><code>UniVec_Core</code>: A subset of UniVec chosen to minimize false positive hits to the vector database</li>
 </ul>
@@ -187,7 +185,7 @@ <h1 id="custom-databases">Custom Databases</h1>
 <pre><code>kraken2-build --download-library archaea --db $DBNAME
 kraken2-build --download-library viral --db $DBNAME</code></pre>
 <p>The above commands would prepare a database that would contain archaeal and viral genomes; the <code>--build</code> option (see below) will still need to be used after downloading these libraries to actually build the database, however.</p>
-<p>(Note that downloading <code>nr</code> or <code>env_nr</code> require use of the <code>--protein</code> option, and that <code>UniVec</code> and <code>UniVec_Core</code> are incompatible with the <code>--protein</code> option.)</p>
+<p>(Note that downloading <code>nr</code> requires use of the <code>--protein</code> option, and that <code>UniVec</code> and <code>UniVec_Core</code> are incompatible with the <code>--protein</code> option.)</p>
 Other genomes can also be added, but such genomes must meet certain requirements:
 <ul>
 <li>Sequences must be in a FASTA file (multi-FASTA is allowed)</li>

docs/MANUAL.markdown

@@ -447,10 +447,6 @@ To build a custom database:
     - `protozoa`: RefSeq complete protozoan genomes/proteins
     - `nr`: NCBI non-redundant protein database
     - `nt`: NCBI non-redundant nucleotide database
-    - `env_nr`: NCBI non-redundant protein database with sequences from
-      large environmental sequencing projects
-    - `env_nt`: NCBI non-redundant nucleotide database with sequences from
-      large environmental sequencing projects
     - `UniVec`: NCBI-supplied database of vector, adapter, linker, and
       primer sequences that may be contaminating sequencing projects and/or
       assemblies
@@ -473,7 +469,7 @@ To build a custom database:
     be used after downloading these libraries to actually build the database,
     however.
 
-    (Note that downloading `nr` or `env_nr` require use of the `--protein`
+    (Note that downloading `nr` requires use of the `--protein`
       option, and that `UniVec` and `UniVec_Core` are incompatible with
       the `--protein` option.)
 

scripts/kraken2-build

@@ -206,8 +206,7 @@ Task options (exactly one must be selected):
   --download-library TYPE    Download partial library
                              (TYPE = one of "archaea", "bacteria", "plasmid",
                              "viral", "human", "fungi", "plant", "protozoa",
-                             "nr", "nt", "UniVec",
-                             "UniVec_Core")
+                             "nr", "nt", "UniVec", "UniVec_Core")
   --special TYPE             Download and build a special database
                              (TYPE = one of "greengenes", "silva", "rdp")
   --add-to-library FILE      Add FILE to library