From 51654f34dd3583f5265d8f331557199d166a82cd Mon Sep 17 00:00:00 2001 From: "Adam R. Rivers" Date: Fri, 15 Sep 2023 14:35:42 -0400 Subject: [PATCH 1/2] updated dockerfiles and fixed soem style errors --- CHANGELOG.md | 16 ++++++++-------- coverage.xml | 7 +++---- docker-images/nonavx/Dockerfile | 5 +++-- docker-images/webapp/Dockerfile | 11 ++++++----- guidemaker/cli.py | 2 +- 5 files changed, 21 insertions(+), 20 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8e392a0..2e6db07 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,11 @@ # v0.4.0 -* changed the cli flag `--filter_by_locus` to `--filter_by_attribute` and added the flag `--attribute_key` so that keys other than the addribute key "locus_tag" can be filtered. -* Changed the cli to add `--raw_output_only`. This option allows the user to just get hte guides that met LSR and distance criteria without doing any parsing of the genome annotation files. -* updated caching for Streamlit 1.26 -* updated GC and position methods for Biopython 1.8.1 -* replaced append methods with concat methods for Pandas 2.1.1 -* output data is now gzipped -* updated Dockerfile to use minimamba base image -* +* changed the cli flag `--filter_by_locus` to `--filter_by_attribute` and added the flag `--attribute_key` so that keys other than the addribute key "locus_tag" can be filtered. +* Changed the cli to add `--raw_output_only`. This option allows the user to just get hte guides that met LSR and distance criteria without doing any parsing of the genome annotation files. +* updated caching for Streamlit 1.26 +* updated GC and position methods for Biopython 1.8.1 +* replaced append methods with concat methods for Pandas 2.1.1 +* output data is now gzipped +* updated Dockerfile to use minimamba base image +* Updates to python dependencies diff --git a/coverage.xml b/coverage.xml index b09e02a..3f4aa78 100644 --- a/coverage.xml +++ b/coverage.xml @@ -1,12 +1,12 @@ - + /Users/rivers/Documents/guidemaker/guidemaker - + @@ -70,7 +70,7 @@ - + @@ -80,7 +80,6 @@ - diff --git a/docker-images/nonavx/Dockerfile b/docker-images/nonavx/Dockerfile index ae82516..a9f1414 100644 --- a/docker-images/nonavx/Dockerfile +++ b/docker-images/nonavx/Dockerfile @@ -16,12 +16,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ build-essential \ python3-dev \ zlib1g-dev \ - git + git && apt-get clean \ + && rm -rf /var/lib/apt/lists/* USER $MAMBA_USER # RUN pip install --no-binary :all: nmslib -RUN git clone -b https://github.com/USDA-ARS-GBRU/GuideMaker.git && cd GuideMaker && pip install . +RUN git clone https://github.com/USDA-ARS-GBRU/GuideMaker.git && cd GuideMaker && pip install . # port on the docker container EXPOSE 8501 diff --git a/docker-images/webapp/Dockerfile b/docker-images/webapp/Dockerfile index 956036d..7f259a6 100644 --- a/docker-images/webapp/Dockerfile +++ b/docker-images/webapp/Dockerfile @@ -13,15 +13,16 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1 USER root RUN apt-get update && apt-get install -y --no-install-recommends \ - build-essential \ - python3-dev \ - zlib1g-dev \ - git + build-essential=12.9 \ + python3-dev=3.9 \ + zlib1g-dev=1.2 \ + git=2.30 && apt-get clean \ + && rm -rf /var/lib/apt/lists/* USER $MAMBA_USER RUN pip install --no-binary :all: nmslib -RUN git clone -b https://github.com/USDA-ARS-GBRU/GuideMaker.git && cd GuideMaker && pip install . +RUN git clone https://github.com/USDA-ARS-GBRU/GuideMaker.git && cd GuideMaker && pip install . # port on the docker container EXPOSE 8501 diff --git a/guidemaker/cli.py b/guidemaker/cli.py index 8b22f90..cce369b 100644 --- a/guidemaker/cli.py +++ b/guidemaker/cli.py @@ -11,7 +11,7 @@ import os import yaml import textwrap -import pandas as pd + import pybedtools from Bio import SeqIO From 2003834194f64aa15fe030f72b8e6eb249d03985 Mon Sep 17 00:00:00 2001 From: "Adam R. Rivers" Date: Fri, 15 Sep 2023 14:39:31 -0400 Subject: [PATCH 2/2] format fix to Readme --- README.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/README.md b/README.md index f38e14d..5e34699 100644 --- a/README.md +++ b/README.md @@ -40,7 +40,6 @@ docker pull ghcr.io/usda-ars-gbru/guidemaker-webapp docker pull ghcr.io/usda-ars-gbru/guidemaker-nonavx ``` - ### Bioconda ```bash @@ -71,10 +70,6 @@ guidemaker -h guidemaker -h ``` - -``` - - ### Dependencies * ``pybedtools``