diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..5d0f124 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,2 @@ +* +!Dockerfile diff --git a/.gitignore b/.gitignore index ec73f2e..bfca5b4 100644 --- a/.gitignore +++ b/.gitignore @@ -71,6 +71,8 @@ docs/_build/ # PyBuilder target/ +.idea/ +tags # pyenv python configuration file .python-version diff --git a/Dockerfile b/Dockerfile index e77472a..bda6a56 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,20 +1,14 @@ -FROM ubuntu:17.10 -MAINTAINER Mike Halagan +FROM python:3.7 +MAINTAINER NMDP Bioinformatics -RUN apt-get update -q \ - && apt-get dist-upgrade -qy \ - && apt-get install -qyy wget curl build-essential cpp git \ - && apt-get -qyy install python3.6 python3-pip python3-dev python3-setuptools uwsgi-plugin-python3 python-mysqldb python3-mysql.connector - -RUN apt-get install python3.6-dev -qy +RUN pip install biopython==1.74 PyMySQL==0.9.3 bson==0.5.8 requests==2.22.0 -RUN cd opt/ && git clone https://github.com/nmdp-bioinformatics/SeqAnn && cd SeqAnn \ - && curl https://bootstrap.pypa.io/get-pip.py | python3.6 \ - && pip install --upgrade pip - -RUN cd opt/SeqAnn && pip install -r requirements.txt \ - && python3.6 setup.py install +RUN apt-get update -q \ + && apt-get install python-mysqldb \ + && apt-get install clustalo -y \ + && apt-get install ncbi-blast+ -y \ + && apt-get autoremove \ + && apt-get clean -RUN apt-get install clustalo -y -RUN apt-get install ncbi-blast+ -y +RUN pip install seq-ann==1.0.5 diff --git a/README.rst b/README.rst index 0181db7..8a6508f 100644 --- a/README.rst +++ b/README.rst @@ -39,6 +39,14 @@ created significantly faster when using a BioSQL database. When a BioSQL databas A BioSQL database containing all of IPD-IMGT/HLA is available on DockerHub_ and can be run on any machine that has docker installed. +Install +------------ + +.. code-block:: shell + + pip install seq-ann + + Parameters ---------- @@ -77,6 +85,13 @@ To annotated a sequence initialize a new ``BioSeqAnn`` object and then pass the The packages `ncbi-blast+` and `clustalo` are required to be installed on your system. + Set variables to BioSQL host/port if using BioSQL. + +.. code-block:: shell + + export BIOSQLHOST="localhost" + export BIOSQLPORT=3306 + .. code-block:: python3 from seqann import BioSeqAnn @@ -131,13 +146,6 @@ annotation is not able to be produced then nothing will be returned. Below is an print(feat, ann.gfe, str(ann.annotation[feat].seq), sep="\t") -Install ------------- - -.. code-block:: shell - - pip install seqann - Dependencies ------------ diff --git a/setup.py b/setup.py index 4037f06..9afc768 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ setup( name='seq-ann', - version='1.0.4', + version='1.0.5', description="Sequence Annotation", long_description=readme, author="NMDP Bioinformatics, CIBMTR",