Merge pull request #72 from Sage-Bionetworks/test

Write GENIE release files to .synapseCache/ add vcf2maf dependency

Dockerfile

@@ -26,7 +26,7 @@ RUN apt-get update && apt-get install -y \
 	libcurl4-openssl-dev
 
 RUN pip3 install --upgrade pip
-RUN pip install synapseclient httplib2 pycrypto
+RUN pip install synapseclient httplib2 pycrypto PyYAML
 RUN pip install pandas numexpr --upgrade
 
 RUN rm /usr/bin/python 

docker/Dockerfile

@@ -32,14 +32,16 @@ RUN apt-get update && apt-get install -y \
 	libffi-dev 
 
 RUN pip3 install --upgrade pip
-RUN pip install synapseclient httplib2 pycrypto
+RUN pip install synapseclient httplib2 pycrypto PyYAML
 RUN pip install pandas numexpr --upgrade
 
 RUN rm /usr/bin/python 
 RUN ln -s /usr/bin/python3 /usr/bin/python 
 
 RUN apt-get install -y cpanminus
 RUN apt-get install -y libmysqlclient-dev
+RUN apt-get install -y libxml2-dev libgd-perl
+
 RUN cpanm CPAN::Meta \
 	Archive::Zip \
 	DBI \

genie/dashboard_table_updater.py

@@ -515,15 +515,17 @@ def run_dashboard(syn, database_mappingdf, release, staging=False, public=False)
 
     '''
     update_release_numbers(syn, database_mappingdf, release = release)
-    update_data_release_file_table(syn, database_mappingdf)
-
-    if not staging and not public:
-        print_clinical_values_difference_table(syn, database_mappingdf)
-        update_sample_difference_table(syn, database_mappingdf)
-        update_data_completeness_table(syn, database_mappingdf)
-        update_database_numbers(syn, database_mappingdf)
-        update_oncotree_code_tables(syn, database_mappingdf)
-        update_wiki(syn,database_mappingdf)
+
+    if not staging:
+        update_data_release_file_table(syn, database_mappingdf)
+        if not public:
+            print_clinical_values_difference_table(syn, database_mappingdf)
+            update_sample_difference_table(syn, database_mappingdf)
+            update_data_completeness_table(syn, database_mappingdf)
+            update_database_numbers(syn, database_mappingdf)
+            update_oncotree_code_tables(syn, database_mappingdf)
+            update_wiki(syn,database_mappingdf)
+
 
 def main():
     parser = argparse.ArgumentParser(description='Update dashboard tables')

genie/database_to_staging.py

@@ -18,7 +18,8 @@
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-GENIE_RELEASE_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)),"GENIE_release")
+#GENIE_RELEASE_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)),"GENIE_release")
+GENIE_RELEASE_DIR = os.path.join(os.path.expanduser("~/.synapseCache"),"GENIE_release")
 CASE_LIST_PATH = os.path.join(GENIE_RELEASE_DIR,'case_lists')
 CNA_CENTER_PATH = os.path.join(GENIE_RELEASE_DIR,"data_CNA_%s.txt")
 SAMPLE_CENTER_PATH = os.path.join(GENIE_RELEASE_DIR,'data_clinical_supp_sample_%s.txt')