Dockerfile updated for 1.0.5 release of seq-ann (#148)

- Tested with Python 3.7.4
- Based on Python Base Image
- Corresponds to 1.0.5 release version on PyPi

Prior to this change,

This change

.dockerignore

@@ -0,0 +1,2 @@
+*
+!Dockerfile

.gitignore

@@ -71,6 +71,8 @@ docs/_build/
 
 # PyBuilder
 target/
+.idea/
+tags
 
 # pyenv python configuration file
 .python-version

Dockerfile

@@ -1,20 +1,14 @@
-FROM ubuntu:17.10
-MAINTAINER Mike Halagan <mhalagan@nmdp.org>
+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
 

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
 ------------

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",