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|
#!/bin/sh
# Generate a script to compile Canu using the Holy Build Box.
echo > build-linux.sh \#\!/bin/bash
echo >> build-linux.sh yum install -y git
echo >> build-linux.sh cd /build/src
echo >> build-linux.sh gmake -j 12 \> ../Linux-amd64.out 2\>\&1
echo >> build-linux.sh cd ..
#echo >> build-linux.sh rm -rf Linux-amd64/obj
#echo >> build-linux.sh tar -cf canu-linux.Linux-amd64.tar canu-linux/README* canu-linux/Linux-amd64
chmod 755 build-linux.sh
echo ""
echo "-- Build Linux and make tarballs."
echo ""
echo "% docker run ..."
docker run \
-v `pwd`:/build \
-t \
-i \
--rm phusion/holy-build-box-64:latest /hbb_exe/activate-exec bash /build/build-linux.sh \
> build-linux.sh.out 2>&1
rm -f build-linux.sh
echo ""
echo "-- Build success?"
echo ""
tail -n 1 build-linux.sh.out | head -n 1
tail -n 2 Linux-amd64.out | head -n 1
# Fetch the Upload Agent and install in our bin/.
if [ ! -e src/pipelines/dx-canu/resources/bin/ua ] ; then
echo ""
echo "-- Fetch UploadAgent."
echo ""
curl -L -R -O https://dnanexus-sdk.s3.amazonaws.com/dnanexus-upload-agent-1.5.31-osx.zip
curl -L -R -O https://dnanexus-sdk.s3.amazonaws.com/dnanexus-upload-agent-1.5.31-linux.tar.gz
tar zxf dnanexus-upload-agent-1.5.31-linux.tar.gz
cp -p dnanexus-upload-agent-1.5.31-linux/ua src/pipelines/dx-canu/resources/bin/
cp -p dnanexus-upload-agent-1.5.31-linux/ua src/pipelines/dx-trio/resources/bin/
#rm -rf dnanexus-upload-agent-1.5.31-linux.tar.gz
rm -rf dnanexus-upload-agent-1.5.31-linux
fi
# Remove the old app.
echo ""
echo "-- Purge previous dx-canu and dx-trio builds."
echo ""
echo "% rm -rf dx-canu/ dx-trio/"
rm -rf dx-canu/ dx-trio/
mkdir -p dx-canu/ dx-trio/
mkdir -p dx-canu/resources/bin/ dx-trio/resources/bin/
mkdir -p dx-canu/resources/usr/bin/ dx-trio/resources/usr/bin/
mkdir -p dx-canu/resources/usr/lib/ dx-trio/resources/usr/lib/
mkdir -p dx-canu/resources/usr/share/ dx-trio/resources/usr/share/
# Package all that up into dx-canu.
echo ""
echo "-- Package new bits into dx-canu and dx-trio builds."
echo ""
echo "% rsync ..."
rsync -a src/pipelines/dx-canu/ dx-canu/
rsync -a Linux-amd64/bin/ dx-canu/resources/usr/bin/
rsync -a Linux-amd64/lib/ dx-canu/resources/usr/lib/
rsync -a Linux-amd64/share/ dx-canu/resources/usr/share/
rsync -a src/pipelines/dx-trio/ dx-trio/
rsync -a Linux-amd64/bin/ dx-trio/resources/usr/bin/
rsync -a Linux-amd64/lib/ dx-trio/resources/usr/lib/
rsync -a Linux-amd64/share/ dx-trio/resources/usr/share/
#rm -fr Linux-amd64/obj Linux-amd64.tar Linux-amd64.tar.gz
#tar -cf Linux-amd64.tar Linux-amd64
#gzip -1v Linux-amd64.tar
#dx rm Linux-amd64.tar.gz
#dx upload Linux-amd64.tar.gz
echo ""
echo "-- Build the DNAnexus apps."
echo ""
echo "% dx build -f dx-canu"
dx build -f dx-canu
echo "% dx build -f dx-trio"
dx build -f dx-trio
exit 0
|
