Merge pull request #22 from broadinstitute/dp-kraken2

kraken2 build fix for protein dbs

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-core:2.1.20
+FROM quay.io/broadinstitute/viral-core:2.1.33
 
 LABEL maintainer "[email protected]"
 

classify/kraken2.py

@@ -62,8 +62,12 @@ def build(self, db, standard_libraries=(), custom_libraries=(), taxdump_out=None
                 util.file.mkdir_p(db)
                 futs.append(executor.submit(shutil.copytree, tax_db, os.path.join(db, 'taxonomy')))
             else:
-                futs.append(executor.submit(self.execute, 'kraken2-build', db, None,
-                    options={'--download-taxonomy': None}))
+                if protein:
+                    futs.append(executor.submit(self.execute, 'kraken2-build', db, None,
+                        options={'--download-taxonomy': None, '--protein': None}))
+                else:
+                    futs.append(executor.submit(self.execute, 'kraken2-build', db, None,
+                        options={'--download-taxonomy': None}))
             # add standard libraries:
             if standard_libraries:
                 for lib in standard_libraries:

docs/requirements.txt

@@ -1,6 +1,6 @@
-Sphinx==1.4.4
-sphinx-argparse==0.1.15
-sphinx_rtd_theme==0.1.9
-matplotlib==2.2.4
-#PyYAML==5.1
+Sphinx>=5.3.0
+sphinx-jinja2-compat
+sphinx-argparse>=0.1.15
+sphinx_rtd_theme>=0.1.9
+matplotlib>=2.2.4
 mock>=2.0.0