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Tool demo #3

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Jan 28, 2017
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8 changes: 4 additions & 4 deletions Galaxy/setupScriptsForGalaxy/GCE-standup.sh
Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@ gcloud compute images create ${TEAMTERI_IMAGE} \
--description="Galaxy_client" \
--source-uri="http://storage.googleapis.com/galaxyproject_images/planemo_machine_smc.06.image.tar.gz"

echo "Creating persistent disk image..."
gcloud compute disks create --size=500GB --zone=${ZONE} ${PERSISTENT_DISK}
#echo "Creating persistent disk image..."
#gcloud compute disks create --size=500GB --zone=${ZONE} ${PERSISTENT_DISK}

echo "Creating client instances, please wait..."
gcloud compute instances create ${GCLOUD_ARGS} ${CLIENT_INSTANCES} \
Expand All @@ -25,5 +25,5 @@ gcloud compute instances create ${GCLOUD_ARGS} ${CLIENT_INSTANCES} \
--image ${TEAMTERI_IMAGE} \
--image-project ${PROJECT} \
--boot-disk-size ${BOOT_DISK_SIZE} \
--disk=name=${PERSISTENT_DISK},device-name=galaxy-data \
--metadata-from-file startup-script=boot.sh
# --disk=name=${PERSISTENT_DISK},device-name=galaxy-data \
# --metadata-from-file startup-script=boot.sh
38 changes: 19 additions & 19 deletions Galaxy/setupScriptsForGalaxy/boot.sh
Original file line number Diff line number Diff line change
@@ -1,22 +1,22 @@
#!/usr/bin/env bash

#cd /opt/galaxy/tools
#git clone https://github.com/Sage-Bionetworks/SMC-Het-Challenge-Examples.git
#service docker restart
#restart_galaxy
cd /opt/galaxy/tools
git clone https://github.com/Sage-Bionetworks/SMC-Het-Challenge-Examples.git
service docker restart
restart_galaxy

mkfs.ext4 -F -E lazy_itable_init=0,lazy_journal_init=0,discard /dev/disk/by-id/google-galaxy-data
mkdir -p /mnt/disks/data
mount -o discard,defaults /dev/disk/by-id/google-galaxy-data /mnt/disks/data
chmod a+w /mnt/disks/data
echo UUID=`sudo blkid -s UUID -o value /dev/disk/by-id/google-galaxy-data` /mnt/disks/data ext4 discard,defaults,
nobootwait 0 2 | tee -a /etc/fstab
cd /mnt/disks/data
apt-get install gcc python-dev python-setuptools
easy_install -U pip
pip uninstall crcmod
pip install -U crcmod

mkdir /mnt/disks/data/dream
chmod a+w /mnt/disks/data/dream
gsutil -m cp -R gs://public-dream-data/* /mnt/disks/data/dream/ &
#mkfs.ext4 -F -E lazy_itable_init=0,lazy_journal_init=0,discard /dev/disk/by-id/google-galaxy-data
#mkdir -p /mnt/disks/data
#mount -o discard,defaults /dev/disk/by-id/google-galaxy-data /mnt/disks/data
#chmod a+w /mnt/disks/data
#echo UUID=`sudo blkid -s UUID -o value /dev/disk/by-id/google-galaxy-data` /mnt/disks/data ext4 discard,defaults,
#nobootwait 0 2 | tee -a /etc/fstab
#cd /mnt/disks/data
#apt-get install gcc python-dev python-setuptools
#easy_install -U pip
#pip uninstall crcmod
#pip install -U crcmod
#
#mkdir /mnt/disks/data/dream
#chmod a+w /mnt/disks/data/dream
#gsutil -m cp -R gs://public-dream-data/* /mnt/disks/data/dream/ &