add compile and hbb scripts

Author: rob-p

scripts/compile.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+set -e
+
+branch=$1
+version=$2
+
+echo "Building rapmap [branch = ${branch}]. Tagging version as ${version}"
+
+# Activate Holy Build Box environment.
+source /hbb_exe/activate
+
+set -x
+
+# Install things we need
+yum install -y --quiet wget
+wget http://download.fedoraproject.org/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm
+rpm -i --quiet epel-release-5-4.noarch.rpm
+#yum install -y --quiet git
+#yum install -y --quiet xz-devel.x86_64
+#yum install -y --quiet bzip2-devel.x86_64
+yum install -y --quiet unzip
+
+curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${branch}.zip -o ${branch}.zip
+unzip ${branch}.zip
+mv RapMap-${branch} RapMap
+cd RapMap
+mkdir build
+cd build
+cmake -DFETCH_BOOST=TRUE ..
+make
+make install
+make test
+cd ../scripts
+bash make-release.sh -v ${version} -n CentOS5
+cd ../RELEASES
+cp *.tar.gz /io/

scripts/make-release.sh

@@ -0,0 +1,76 @@
+#!/bin/bash
+
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+  DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+  SOURCE="$(readlink "$SOURCE")"
+  [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+host=
+version=
+
+while getopts "v:n:" opt; do
+  case $opt in
+    n)
+      echo "Host is $OPTARG" >&2
+      host=$OPTARG
+      ;;
+    v)
+      echo "Version is $OPTARG" >&2
+      version=$OPTARG
+      ;;
+    \?)
+      echo "Invalid option: -$OPTARG" >&2
+      exit 1
+      ;;
+  esac
+d``one
+
+echo -e "Preparing binary release\n=====================\n"
+echo -e "Version = ${version}"
+echo -e "Host = ${host}"
+
+# create the binary directory 
+betaname=RapMap-${version}_${host}
+mkdir ${DIR}/../RELEASES
+mkdir ${DIR}/../RELEASES/${betaname}
+mkdir ${DIR}/../RELEASES/${betaname}/bin
+mkdir ${DIR}/../RELEASES/${betaname}/lib
+
+echo -e "Copying over the binary\n"
+cp ${DIR}/../bin/rapmap ${DIR}/../RELEASES/${betaname}/bin/
+
+# copy other dependencies (shared libraries)
+#echo -e "Copying over other shared library dependencies\n"
+#bash ${DIR}/../scripts/cpld.bash ${DIR}/../bin/salmon ${DIR}/../RELEASES/${betaname}/lib/
+#echo -e "Removing dangerous dependencies\n"
+#rm ${DIR}/../RELEASES/${betaname}/lib/libc.so.6
+#rm ${DIR}/../RELEASES/${betaname}/lib/ld-linux-x86-64.so.2
+#rm ${DIR}/../RELEASES/${betaname}/lib/libdl.so.2
+#rm ${DIR}/../RELEASES/${betaname}/lib/libpthread*.so.*
+
+# now make the tarball
+echo -e "Making the tarball\n"
+cd ${DIR}/../RELEASES
+tar czvf ${betaname}.tar.gz ${betaname}
+
+echo -e "Done making release!"
+
+#echo -e "Pushing the tarball to GitHub\n"
+## Since it's currently unclear to me how to overwrite an asset via the GitHub
+## API, the following code deletes the old asset, and uploads the new one in its place
+#
+## Get the previous asset id of the tarball
+#echo -e "Getting previous asset ID\n"
+#ASSETID=`curl -s -X GET https://api.github.com/repos/COMBINE-lab/salmon/releases/1263754/assets | grep "\"id" | head -1 | awk '{gsub(/,$/,""); print $2}'`
+#
+## Delete the previous tarball
+#echo -e "Deleting previous asset\n"
+#curl -X DELETE -H "Authorization: token ${SALMON_PUSH_KEY}" https://api.github.com/repos/COMBINE-lab/salmon/releases/assets/$ASSETID
+#
+## Upload the new tarball
+#echo -e "Uploading new asset\n"
+#curl -X POST --data-binary "@SalmonBeta-latest_ubuntu-12.04.tar.gz" https://uploads.github.com/repos/COMBINE-lab/salmon/releases/1263754/assets?name=SalmonBeta-latest_ubuntu-12.04.tar.gz --header "Content-Type:application/gzip" -H "Authorization: token ${SALMON_PUSH_KEY}"
+#echo -e "Done!\n"