Merge pull request #59 from openvar/requests

Requests

Author: Peter J. Freeman

REQUIREMENTS.txt

@@ -1,6 +1,7 @@
 git+https://github.com/openvar/vv_hgvs.git@1.2.5.vv1#egg=vvhgvs
-git+https://github.com/openvar/variantValidator@1.0.4#egg=VariantValidator
-git+https://github.com/openvar/variantFormatter@1.0.2#egg=VariantFormatter
+git+https://github.com/openvar/variantValidator@v1.0.4#egg=VariantValidator
+git+https://github.com/openvar/variantFormatter@v1.0.2#egg=VariantFormatter
+biopython==1.74
 flask
 flask-restplus
 gunicorn

configuration/docker.ini

@@ -22,8 +22,8 @@ console = DEBUG
 file = ERROR
 
 [Entrez]
-email = <YOUR EMAIL ADDRESS>
-api_key = <YOUR API KEY>
+email = admin@variantvalidator.org
+api_key = a991783f8c1e9e1958d1e6bd90b6f4046f08
 
 
 # <LICENSE>

docker-compose.yml

@@ -37,11 +37,12 @@ services:
     expose:
       - "5000"
       - "8000"
+
 volumes:
   seqdata:
   share:
     driver: local
     driver_opts:
       type: 'none'
       o: 'bind'
-      device: '${HOME}/share'
+      device: '${HOME}/variantvalidator_data/share'

docs/DOCKER.md

@@ -14,6 +14,7 @@ $ git clone https://github.com/openvar/rest_variantValidator
 ```
 
 Once the repository has been cloned, cd into the rest_variantValidator directory that the clone creates.
+
 ```bash
 $ cd rest_variantValidator/
 ``` 
@@ -44,7 +45,8 @@ $ docker-compose pull
 
 - Create a directory for sharing resources between your computer and the container
 ```bash
-$ mkdir ~/share
+$ mkdir ~/variantvalidator_data
+$ mkdir ~/variantvalidator_data/share
 ```
 i.e. a directory called share in your home directory
 

setup.py

@@ -57,9 +57,10 @@
         "requests",
         "dicttoxml",
         "vvhgvs @ git+https://github.com/openvar/vv_hgvs.git@1.2.5.vv1#egg=vvhgvs",
-        "VariantValidator @ git+https://github.com/openvar/variantValidator.git@1.0.4#egg=VariantValidator",
-        "VariantFormatter @ git+https://github.com/openvar/variantFormatter.git@1.0.2#egg=VariantFormatter",
+        "VariantValidator @ git+https://github.com/openvar/variantValidator.git@v1.0.4#egg=VariantValidator",
+        "VariantFormatter @ git+https://github.com/openvar/variantFormatter.git@v1.0.2#egg=VariantFormatter",
         "biocommons.seqrepo>=0.5.1",
+        "biopython==1.74",
     ],
     setup_requires=[
         "setuptools_scm",