Docker2

.travis.yml

@@ -48,6 +48,7 @@ before_script:
 script:
     - pylint $TRAVIS_BUILD_DIR/docker/vcf_combiner/usr/bin/combine_vcf.py
     - pytest $TRAVIS_BUILD_DIR/docker/vcf_combiner/usr/bin/combine_vcf.py
+    - bash -n $TRAVIS_BUILD_DIR/docker/genomicsdb_builder/usr/bin/build_genomicsdb  
     - cd $GENOMICSDB_BUILD_DIR
     - cmake $TRAVIS_BUILD_DIR -DBUILD_JAVA=1 -DCMAKE_BUILD_TYPE=Coverage -DCMAKE_INSTALL_PREFIX=$GENOMICSDB_INSTALL_DIR -DLIBCSV_DIR=$TRAVIS_BUILD_DIR/dependencies/libcsv -DGENOMICSDB_RELEASE_VERSION=$GENOMICSDB_RELEASE_VERSION -DMAVEN_QUIET=True
     - ln -s $TRAVIS_BUILD_DIR/tests

docker/genomicsdb_builder/.dockerignore

@@ -0,0 +1,2 @@
+# no build
+/build_src/

docker/genomicsdb_builder/Dockerfile

@@ -0,0 +1,45 @@
+# The MIT License (MIT)
+# Copyright (c) 2016-2017 Intel Corporation
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# The code utilized some features of RedHat pre-built container
+
+FROM centos:7
+
+LABEL vendor="Intel Inc." name="GenomicsDB Builder" version="1.0" description="Build GenomicsDB"
+
+RUN yum install -y --setopt=tsflags=nodocs centos-release-scl && \
+    yum-config-manager --enable rhel-server-rhscl-7-rpms && \
+    yum install -y devtoolset-4 && \
+    yum install -y --setopt=tsflags=nodocs epel-release &&  \
+    yum repolist && \
+    yum install -y --setopt=tsflags=nodocs cmake git.x86_64 libcsv libcsv-devel mpich-devel openssl-devel zlib-devel unzip.x86_64 && \  
+    yum install -y python34.x86_64 && \
+    yum clean all
+
+ENV BASH_ENV=/etc/profile.d/cont-env.sh PATH=$PATH:/usr/lib64/mpich/bin HOME=/home/default
+
+WORKDIR /home/default
+
+ADD ./usr /usr
+ADD ./etc /etc
+ADD ./root /root
+
+ENTRYPOINT ["/usr/bin/container-entrypoint"]
+CMD ["build_genomicsdb"]

docker/genomicsdb_builder/README.md

@@ -0,0 +1,23 @@
+### GenomicsDB Building Docker
+
+The centos-build is the source code for building a GenomicsDB building environment Docker image. The details about GenomicsDB building environment can be found at [GenomicsDB Wiki]( https://github.com/Intel-HLS/GenomicsDB/wiki/Compiling-GenomicsDB#building.)
+
+To create a GenomicsDB building environment Docker image, run the following command:
+
+<code>docker build -t name_of_the_builder_image --no-cache .</code>
+
+Once the image is created. You can build the latest GenomicsDB executables by running:
+
+<code>docker run -it -v /path/2/output/:/output/ [-e  GDB_BRANCH=branch_name_default_is_master] name_of_the_builder_image</code>
+
+In this case, the docker container builds GenomicsDB with the following options:
+
+* CMAKE_BUILD_TYPE=Release
+* DO_PROFILING=False
+* DISABLE_OPENMP=True
+* BUILD_JAVA=False
+* DO_PROFILING=False  
+* CMAKE_INSTALL_PREFIX=/output/
+* PROTOBUF_LIBRARY=dont_worry_the_docker_manage_it
+
+You can pass GenomicsDB building options via docker run command arguments. The docker will pass your arguments to cmake. Since the docker builds protobuf library internally, you just ignore the PROTOBUF_LIBRARY option.

docker/genomicsdb_builder/etc/profile.d/cont-env.sh

@@ -0,0 +1 @@
+source /usr/share/cont-lib/cont-env.sh

docker/genomicsdb_builder/root/.bashrc

@@ -0,0 +1 @@
+source /usr/share/cont-lib/cont-env.sh

docker/genomicsdb_builder/usr/bin/build_genomicsdb

@@ -0,0 +1,99 @@
+#! /bin/bash
+# The MIT License (MIT)
+# Copyright (c) 2017 Intel Corporation
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+if [ ! -d /output ]; then
+  echo 'can not find /output/ exit...'
+  return 2
+fi
+export BUILD_ROOT=${HOME}/build_src
+export PROTOBUF_LIBRARY=$BUILD_ROOT/protobuf_build
+echo "build_home=$build_home, PROTOBUF_LIBRARY=$PROTOBUF_LIBRARY, GenomicsDB_HOME=$GenomicsDB_HOME"
+
+protobuf_to_dir=/output
+genomicsdb_to_dir=/output
+
+# make protobuf
+build_proto_buf() {
+  echo "+++ Building protobuf at ${PROTOBUF_LIBRARY}..."
+  mkdir -p /output/protobuf
+  mkdir -p ${PROTOBUF_LIBRARY} && pushd ${PROTOBUF_LIBRARY} >/dev/null 2>&1
+  git clone https://github.com/google/protobuf.git
+  cd protobuf
+  git checkout 3.0.x
+  ./autogen.sh
+  ./configure --prefix=$protobuf_to_dir --with-pic
+  if [ -f ./Makefile ]; then
+     make && make install
+     basename $(ls $protobuf_to_dir/bin/protoc)
+     find $protobuf_to_dir/lib/ -name 'libproto*' -type f -exec basename {} \;
+     echo "--- Done building protobuf"
+     popd >/dev/null 2>&1
+     return 0
+  else
+     popd >/dev/null 2>&1
+     echo "ERROR: build_proto_buf not find Makefile"
+     return -1
+  fi
+}
+
+# make genomicsdb
+build_gdb() {
+  echo
+  echo "+++ Building GenomicsDB at ${GenomicsDB_HOME}..."
+  git clone --recursive https://github.com/Intel-HLS/GenomicsDB.git
+  ws=GenomicsDB/build
+  mkdir -p $ws && pushd $ws >/dev/null 2>&1
+  branch=${GDB_BRANCH:=master}
+  git checkout $branch
+  git branch
+  if [ $# -gt 0 ]; then
+    cmake --warn-uninitialized --debug-output .. -DCMAKE_INSTALL_PREFIX=$genomicsdb_to_dir -DPROTOBUF_LIBRARY=$protobuf_to_dir $@
+  else
+    cmake --warn-uninitialized --debug-output .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$genomicsdb_to_dir -DDO_PROFILING=False -DPROTOBUF_LIBRARY=$protobuf_to_dir -DDISABLE_OPENMP=True -DBUILD_JAVA=False -DDO_PROFILING=False
+  fi
+
+  if [ -f ./Makefile ]; then
+     make && make  install
+     echo "INFO: Successfully built GenomicsDB... run test"
+     ../tests/run.py $PWD $genomicsdb_to_dir
+     popd >/dev/null 2>&1
+     return 0
+  else
+     echo "ERROR: build_gdb not find Makefile"
+     popd >/dev/null 2>&1
+     return -1
+  fi
+}
+
+#source /opt/rh/devtoolset-4/enable
+gcc --version
+
+mkdir -p ${BUILD_ROOT} && pushd ${BUILD_ROOT} >/dev/null 2>&1
+build_proto_buf
+retst=$?
+if [ $retst -eq 0 ]; then
+  build_gdb $@
+  retst=$?
+  rsync -az $genomicsdb_to_dir /usr
+fi
+[[ $retst -eq 0 ]] && echo "DONE: built GenomicsDB" || echo "FAIL: cannot build GenomicsDB" 
+popd >/dev/null 2>&1
+return $retst

docker/genomicsdb_builder/usr/bin/container-entrypoint

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+. /usr/share/cont-lib/cont-lib.sh
+
+cont_debug "command: $*"
+
+__cont_source_scripts "/usr/share/cont-entry"
+
+test -z "$*" && set -- bash
+exec "$@"

docker/genomicsdb_builder/usr/bin/container-usage

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+# TODO: support API for executable help scripts
+cat /usr/share/cont-docs/*.txt 2>/dev/null
+
+

docker/genomicsdb_builder/usr/share/cont-docs/70-general.txt

@@ -0,0 +1,20 @@
+General container help
+----------------------
+
+Run `docker run THIS_IMAGE container-usage` to get this help.
+
+Run `docker run -ti THIS_IMAGE bash` to obtain interactive shell.
+
+Run `docker exec -ti CONTAINERID container-entrypoint` to access already running container.
+
+In order to get the container ID after running the image, pass `--cidfile=`
+option to the `docker run` command. That will instruct Docker to write
+a file with the container ID.
+
+You may try `-e CONT_DEBUG=VAL` with VAL up to 3 to get more verbose debugging
+info.
+
+
+Report bugs to <http://bugzilla.redhat.com>.
+
+

docker/genomicsdb_builder/usr/share/cont-docs/README

@@ -0,0 +1 @@
+Files '*.txt' are automatically read and added to 'container-usage' output.

docker/genomicsdb_builder/usr/share/cont-entry/cont-env.sh

@@ -0,0 +1 @@
+source /usr/share/cont-lib/cont-env.sh

docker/genomicsdb_builder/usr/share/cont-layer/common/env/enabledevtoolset-4.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+# M:R: this file was part of Red Hat samples
+source scl_source enable devtoolset-4

docker/genomicsdb_builder/usr/share/cont-lib/autoload/README

@@ -0,0 +1,2 @@
+All '*.sh' files in this directory will be automatically sourced together with
+cont-lib.sh script.

docker/genomicsdb_builder/usr/share/cont-lib/cont-env.sh

@@ -0,0 +1,6 @@
+. /usr/share/cont-lib/cont-lib.sh
+
+cont_debug "changing environment variables"
+
+cont_source_hooks env common
+

docker/genomicsdb_builder/usr/share/cont-lib/cont-lib.sh

@@ -0,0 +1,97 @@
+__cont_source_scripts()
+{
+    local i
+    local dir="$1"
+    for i in "$dir"/*.sh; do
+        if test -r "$i"; then
+            . "$i"
+        fi
+    done
+}
+
+
+# CONT_SOURCE_HOOKS HOOKDIR [PROJECT]
+# -----------------------------------
+# Source '*.sh' files from the following directories (in this order):
+#   a. /usr/share/cont-layer/PROJECT/HOOK/
+#   b. /usr/share/cont-volume/PROJECT/HOOK/
+#
+# The PROJECT argument is optional because it may be set globally by
+# $CONT_PROJECT environment variable.  The need for PROJECT argument is
+# basically to push people to install script into theirs own directories,
+# which will allow easier multi-project containers maintenance.
+cont_source_hooks()
+{
+    local i dir
+    local hook="$1"
+    local project="$CONT_PROJECT"
+    local dir
+
+    test -z "$hook" && return
+    test -n "$2" && project="$2"
+
+    for dir in /usr/share/cont-layer /usr/share/cont-volume; do
+        dir="$dir/$project/$hook"
+        cont_debug2 "loading scripts from $dir"
+        __cont_source_scripts "$dir"
+    done
+}
+
+__cont_msg()
+{
+    echo "$*" >&2
+}
+
+
+__cont_dbg()
+{
+    test -z "$CONT_DEBUG" && CONT_DEBUG=0
+    test "$CONT_DEBUG" -lt "$1" && return
+    local lvl="$1"
+    shift
+    __cont_msg "debug_$lvl: $*"
+}
+
+
+cont_warn()   { __cont_msg "warn: $*" ; }
+cont_error()  { __cont_msg "error: $*"; }
+cont_debug()  { __cont_dbg 1 "$*" ; }
+cont_debug2() { __cont_dbg 2 "$*" ; }
+cont_debug3() { __cont_dbg 3 "$*" ; }
+
+
+__cont_encode_env()
+{
+    local i
+    for i in $1
+    do
+        eval local val="\$$i"
+        printf ": \${%s=%q}\n" "$i" "$val"
+    done
+}
+
+
+# CONT_STORE_ENV VARIABLES FILENAME
+# ---------------------------------
+# Create source-able script conditionally setting specified VARIABLES by
+# inheritting the values from current environment; Create the file on path
+# FILENAME.  Already existing variables will not be changed by sourcing the
+# resulting script.  The argument VARIABLES expects list of space separated
+# variable names.
+#
+# Usage:
+#   $ my_var=my_value
+#   $ my_var2="my value2"
+#   $ cont_store_env "my_var my_var2" ~/.my-environment
+#   $ cat ~/.my-environment
+#   : ${my_var=my_value}
+#   : ${my_var2=my\ value2}
+cont_store_env()
+{
+    cont_debug "creating env file '$2'"
+    __cont_encode_env "$1" > "$2" \
+        || cont_warn "can't store environment $1 into $2 file"
+}
+
+
+__cont_source_scripts "/usr/share/cont-lib/autoload"