Merge branch 'hotfix/1.0.2'

Author: sb43

.travis.yml

@@ -1,4 +1,10 @@
 dist: trusty
+# safelist
+branches:
+  only:
+  - master
+  - develop
+  - /^\d+\.\d+\.\d+$/
 
 notifications:
   email: false

CHANGES.md

@@ -1,3 +1,9 @@
+## 1.0.2
+* Updated docker to install from release dist 
+* added merged annotation list 
+* Works with symlinked vcf files provided tabix index is at same location
+## 1.0.1
+* Updated docker file
 ## 1.0.0
 * First working release
 

Dockerfile

@@ -1,74 +1,43 @@
-FROM  ubuntu:20.04 as builder
-USER root
+FROM python:3.7-slim as builder
 
 MAINTAINER  [email protected]
 
-ENV ANNOTATEVCF_VER '1.0.0'
+ENV ANNOTATEVCF_VER '1.0.2'
 
 # install system tools
-RUN apt-get -yq update
-RUN apt-get install -yq --no-install-recommends \
-locales \
-g++ \
-make \
-gcc \
-pkg-config \
-python3 python3-dev python3-pip python3-setuptools python3-wheel \
-zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev \
-bcftools tabix git
 
-ENV CGP_OPT /opt/wtsi-cgp
-RUN mkdir $CGP_OPT
-ENV PYTHONPATH $CGP_OPT/python-lib/lib/python3.6/site-packages
+ENV CGP_OPT /opt/wtsi-cgp/venv
+
+RUN python -m venv $CGP_OPT
+# Make sure we use the virtualenv:
+ENV PATH $CGP_OPT/bin:$CGP_OPT/python-lib/bin:$PATH
+ENV PYTHONPATH $CGP_OPT/python-lib/lib/python3.7/site-packages
+RUN pip3 install --upgrade setuptools
 
-RUN locale-gen en_US.UTF-8
-RUN update-locale LANG=en_US.UTF-8
-ENV LC_ALL en_US.UTF-8
-ENV LANG en_US.UTF-8
+RUN pip3 install --install-option="--prefix=$CGP_OPT/python-lib" https://github.com/cancerit/annotateVCF/archive/${ANNOTATEVCF_VER}.tar.gz
 
-COPY requirements.txt $CGP_OPT/requirements.txt
-RUN pip3 --no-cache-dir install -r $CGP_OPT/requirements.txt
-# install annotatevcf
-RUN pip3 --no-cache-dir install https://github.com/cancerit/annotateVCF/releases/download/${ANNOTATEVCF_VER}/annotateVcf-${ANNOTATEVCF_VER}-py3-none-any.whl
+COPY . .
 
-COPY ..
+RUN python3 setup.py sdist
+RUN pip3 install --install-option="--prefix=$CGP_OPT/python-lib" dist/$(ls -1 dist/)
 
-FROM ubuntu:20.04
+FROM python:3.7-slim
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Sanger Institute" \
-      version="1.0.0" \
+      version="$ANNOTATEVCF_VER" \
       description="Tool to perform vcf file annotation"
 
-### security upgrades and cleanup
+# Make sure we use the virtualenv:
+ENV CGP_OPT /opt/wtsi-cgp/venv
+RUN mkdir -p $CGP_OPT
+COPY --from=builder $CGP_OPT $CGP_OPT
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends \
-apt-transport-https \
-locales \
-ca-certificates \
-time \
-unattended-upgrades \
-python3 \
-zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev && \
-unattended-upgrade -d -v && \
-apt-get remove -yq unattended-upgrades && \
-apt-get autoremove -yq
-
-
-RUN locale-gen en_US.UTF-8
-RUN update-locale LANG=en_US.UTF-8
-
-ENV CGP_OPT /opt/wtsi-cgp
+    bcftools tabix
+#set PATHS 
 ENV PATH $CGP_OPT/bin:$CGP_OPT/python-lib/bin:$PATH
-ENV PYTHONPATH $CGP_OPT/python-lib/lib/python3.6/site-packages
-ENV LD_LIBRARY_PATH $OPT/lib
-ENV LC_ALL en_US.UTF-8
-ENV LANG en_US.UTF-8
-
-RUN mkdir -p $CGP_OPT
-COPY --from=builder $CGP_OPT $CGP_OPT
-
+ENV PYTHONPATH $CGP_OPT/python-lib/lib/python3.7/site-packages
 ## USER CONFIGURATION 
-
 RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
 
 USER ubuntu

annotate/config/drvData.json

@@ -1,7 +1,7 @@
 {
   "drv_genes":"lof_genes_v1.0.txt",
   "drv_genes_prev":"lof_genes_previous_symbol.v1.0.txt",
-  "drv_mut":"driver_mutations_grch38_v1.0.tsv.gz",
+  "drv_mut":"driver_mutations_grch38_v1.0.2.tsv.gz",
   "lof_consequences":["stop_lost","start_lost","ess_splice","frameshift","nonsense"],
   "header_info":"vcf_info.txt",
   "genome_loc":"genome_grch38.tab.gz"

annotate/config/drvData/driver_mutations_grch38_v1.0.2.tsv.gz

@@ -40,7 +40,9 @@ def input_checker(infile):
           checks user input file and returns it's type
         """
         try:
-            if os.path.isfile(infile):
+            if os.path.exists(infile) and os.path.islink(infile):
+                return 'y'
+            elif os.path.isfile(infile):
                 return 'y'
             else:
                 return None
@@ -250,4 +252,4 @@ def tempdir(mypath):
             try:
                 shutil.rmtree(path)
             except IOError:
-                sys.stderr.write('Failed to clean up temp dir {}'.format(path))
+                sys.stderr.write('Failed to clean up temp dir {}'.format(path))

annotate/config/drvData/driver_mutations_grch38_v1.0.2.tsv.gz.tbi

@@ -3,7 +3,7 @@
 from setuptools import setup
 
 config = {
-    'version': '1.0.0',
+    'version': '1.0.2',
     'name': 'annotateVcf',
     'description': 'Tool to annotate vcf files...',
     'author': 'Shriram Bhosle',