Add pipeline_runner files

.gitignore

@@ -28,6 +28,6 @@ pipeline-logs
 sql-dumps
 
 .vscode/
-pipeline_runner/
+# pipeline_runner/
 pipeline_runner/*/.github
 */*.zip

pipeline_runner/download_reference_data.sh

@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+
+set -x -e
+
+BUILD_VERSION=$1
+
+# download VEP cache
+mkdir -p /vep_data/homo_sapiens
+cd /vep_data
+CACHE_FILE=homo_sapiens_vep_104_GRCh${BUILD_VERSION}.tar.gz
+curl -LO "http://ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/${CACHE_FILE}"
+tar xzf "${CACHE_FILE}"
+rm "${CACHE_FILE}"
+
+# download loftee reference data
+mkdir -p "/vep_data/loftee_data/GRCh${BUILD_VERSION}"
+cd "/vep_data/loftee_data/GRCh${BUILD_VERSION}"
+LOFTEE_FILE=GRCh${BUILD_VERSION}.tar
+gsutil cp "gs://seqr-reference-data/vep_data/loftee-beta/${LOFTEE_FILE}" .
+tar xf "${LOFTEE_FILE}"
+rm "${LOFTEE_FILE}"
+
+# download seqr reference data
+REF_DATA_HT=combined_reference_data_grch${BUILD_VERSION}.ht
+CLINVAR_HT=clinvar.GRCh${BUILD_VERSION}.ht
+mkdir -p "/seqr-reference-data/GRCh${BUILD_VERSION}/${REF_DATA_HT}"
+mkdir -p "/seqr-reference-data/GRCh${BUILD_VERSION}/${CLINVAR_HT}"
+cd "/seqr-reference-data/GRCh${BUILD_VERSION}"
+gsutil -m rsync -r "gs://seqr-reference-data/GRCh${BUILD_VERSION}/all_reference_data/${REF_DATA_HT}" "./${REF_DATA_HT}"
+gsutil -m rsync -r "gs://seqr-reference-data/GRCh${BUILD_VERSION}/clinvar/${CLINVAR_HT}" "./${CLINVAR_HT}"

pipeline_runner/ensembl-vep-release-104/.travis.yml

@@ -0,0 +1,74 @@
+language: "perl"
+
+perl:
+  - "5.10"
+  - "5.14"
+  - "5.18"
+  - "5.22"
+  - "5.26"
+
+env:
+  matrix:
+  - COVERALLS=true  DB=mysql
+  global:
+  - secure: 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
+
+sudo: required
+dist: trusty
+group: deprecated
+
+addons:
+  apt:
+    packages:
+      - unzip
+      - mysql-server-5.6
+      - apache2
+      - libmysqlclient-dev
+      - libpng12-dev
+      - libssl-dev
+      - openssl
+      - mysql-client-5.6
+      - mysql-client-core-5.6
+
+before_install:
+  - export ENSEMBL_BRANCH=release/104
+  - git clone --branch release/103 --depth 1 https://github.com/Ensembl/ensembl-test.git
+  - git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl.git
+  - git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl-io.git
+  - git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl-funcgen.git
+  - git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl-variation.git
+
+  - export CWD=$PWD
+  - export DEPS=$HOME/dependencies
+  - mkdir -p $DEPS
+  - cd $DEPS
+  - $CWD/travisci/get_dependencies.sh
+  - cd $CWD
+
+install:
+  - export CWD=$PWD
+  - export DEPS=$HOME/dependencies
+  - export KENT_SRC="$DEPS/kent-335_base/src"
+  - export HTSLIB_DIR="$DEPS/htslib"
+  - export MACHTYPE=$(uname -m)
+  - export CFLAGS="-fPIC"
+  - export PERL5LIB=$DEPS/bioperl-live:$PERL5LIB
+  - cd $DEPS
+  - $CWD/travisci/build_c.sh
+  - cd $CWD
+  - cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
+  - cpanm --quiet --installdeps --with-recommends --notest .
+  - cpanm --quiet -n Devel::Cover::Report::Coveralls
+  - cp travisci/MultiTestDB.conf.travisci  t/MultiTestDB.conf
+
+script: "./travisci/harness.sh"
+
+jobs:
+  include:
+    - stage: trigger_dependent_builds
+      script: ./travisci/trigger-dependent-build.sh
+
+notifications:
+  email:
+    on_success: always
+    on_failure: always

pipeline_runner/ensembl-vep-release-104/.version/ensembl

@@ -0,0 +1,2 @@
+release 104
+sub 1af1dce3518d6af00df04983993deefa01ec2276

pipeline_runner/ensembl-vep-release-104/.version/ensembl-funcgen

@@ -0,0 +1,2 @@
+release 104
+sub 59ae779072d054dc419a8bcb25df70662c71e065

pipeline_runner/ensembl-vep-release-104/.version/ensembl-io

@@ -0,0 +1,2 @@
+release 104
+sub 1d3bb6e77627abee044c4a1268e2be836cd921b5

pipeline_runner/ensembl-vep-release-104/.version/ensembl-variation

@@ -0,0 +1,2 @@
+release 104
+sub 6154f8ba2a8499bbedde5211fb264c9c849a93d0