From 8b4380f173959ad5b42f7d7f674cb8d3ab54d986 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Thu, 18 Jun 2020 10:29:55 -0400 Subject: [PATCH 1/3] protein flag for downloading taxonomy too?? --- classify/kraken2.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/classify/kraken2.py b/classify/kraken2.py index ef47a644..9f10ce47 100644 --- a/classify/kraken2.py +++ b/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: From 689a4b1fc9ee0d290d169e01474187d0da610038 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Mon, 12 Dec 2022 10:45:48 -0500 Subject: [PATCH 2/3] bump core --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 664d70ac..0aa62bd9 100644 --- a/Dockerfile +++ b/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 "viral-ngs@broadinstitute.org" From 20f9d67b17fb2cbed4c038f785328bb42472daa1 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Mon, 12 Dec 2022 10:46:21 -0500 Subject: [PATCH 3/3] fix sphinx/rtd build --- docs/requirements.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 45de2340..02d99453 100644 --- a/docs/requirements.txt +++ b/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