MAINT: Clean up shared resources in sVEP

* Removed symlinks and created script for producing layers

* Lambda functions updated to use these layers to access shared resources instead of including in lambda build

.gitignore

@@ -4,3 +4,14 @@ terraform.tfstate
 .idea/
 .DS_Store
 builds
+
+# python lambda layers
+layers/python_libraries/python
+layers/binaries/bin/*
+layers/binaries/lib/*
+
+# Build files
+*.zip
+*.pyc
+build
+libraries

init.sh

@@ -0,0 +1,41 @@
+set -ex
+REPOSITORY_DIRECTORY="${PWD}"
+LIBRARIES="${REPOSITORY_DIRECTORY}/libraries"
+SOURCE="${LIBRARIES}/source"
+
+# Clean sbeacon-libraries
+if [ -d "${LIBRARIES}" ]
+  then
+    rm -rf "${LIBRARIES}"
+fi
+
+mkdir "${LIBRARIES}"
+mkdir "${SOURCE}"
+
+#
+# building lambda layers
+#
+
+# tabix
+cd ${SOURCE}
+git clone --recursive --depth 1 --branch develop https://github.com/samtools/htslib.git 
+cd htslib && autoreconf && ./configure --enable-libcurl && make
+cd ${REPOSITORY_DIRECTORY}
+mkdir -p layers/binaries/lib
+mkdir -p layers/binaries/bin
+# TODO check what libraries are missing and add only those
+ldd ${SOURCE}/htslib/tabix | awk 'NF == 4 { system("cp " $3 " ./layers/binaries/lib") }'
+cp ${SOURCE}/htslib/tabix ./layers/binaries/bin/
+
+# bcftools
+cd ${SOURCE}
+git clone --recursive --depth 1 --branch develop https://github.com/samtools/bcftools.git
+cd bcftools && autoreconf && ./configure && make
+cd ${REPOSITORY_DIRECTORY}
+mkdir -p layers/binaries/lib
+mkdir -p layers/binaries/bin
+ldd ${SOURCE}/bcftools | awk 'NF == 4 { system("cp " $3 " ./layers/binaries/lib") }'
+cp ${SOURCE}/bcftools/bcftools ./layers/binaries/bin/
+
+# python libraries layer
+cd ${REPOSITORY_DIRECTORY}

lambda/concat/lambda_function.py

@@ -2,7 +2,7 @@
 
 import boto3
 
-from lambda_utils import get_sns_event, sns_publish
+from shared.utils import get_sns_event, sns_publish
 
 
 # AWS clients and resources