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Creating an AMI on EC2 (view source)

Revision as of 13:08, 17 June 2013

209 bytes added ,  13:08, 17 June 2013
→‎Configure the Host to be Usable
Line 140: Line 140:  
<code>
 
<code>
 
ubuntu@ip-10-254-60-210:~$ sudo more /etc/rc.local
 
ubuntu@ip-10-254-60-210:~$ sudo more /etc/rc.local
−
  #!/bin/sh  
+
#!/bin/sh  
−
  USER=ubuntu
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#
−
  THOUSANDG=/mnt/1000g
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# rc.local
−
  FILES3=passwd-s3fs
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#
−
  S3ERR=/tmp/s3fs.err
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# This script is executed at the end of each multiuser runlevel.
−
   
+
# Make sure that the script will "exit 0" on success or any other
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   #    Set up for GotCloud   Assumes /dev/xvdf has reference files for GotCloud
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# value on error.
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   mkdir -p /gotcloud
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#
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   mount /dev/xvdf /gotcloud
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# In order to enable or disable this script just change the execution
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   if [ ! -d /gotcloud/gotcloud.ref ]; then
+
# bits.
 +
#
 +
# By default this script does nothing.
 +
USER=ubuntu
 +
THOUSANDG=/mnt/1000g
 +
FILES3=/etc/passwd-s3fs     # Where s3fs access info will live
 +
S3ERR=/tmp/s3fs.err
 +
#  These are needed for s3fs access
 +
AWSACCESSKEYID=AKIAxxxxxxZ3YCZF2Q
 +
AWSSECRETACCESSKEY=ft1eJa3WxxxxxxxNlbA08x/G8iMqkMIkJjFCIGf
 +
 
 +
 
 +
#    Check that we have swap set up
 +
a=`swapon -s | grep -v File`
 +
if [ "$a" = "" ]; then
 +
  echo "#######################################################"
 +
  echo "#  You have no SWAP file set up"
 +
  echo ""
 +
  echo "# swap=/mnt/swapfile"
 +
  echo "#  sudo dd if=/dev/zero of=$swap bs=1073741824 count=20"
 +
  echo "#  sudo chown root:root $swap"
 +
  echo "#  sudo mkswap $swap"
 +
  echo "#  sudo chmod 0600 $swap"
 +
  echo "#  sudo swapon $swap"
 +
  echo ""
 +
  echo "#  If need be, add to /etc/fstab"
 +
  echo "#  echo "$swap  none swap sw  0  0" >> /etc/fstab"
 +
   echo "#######################################################"
 +
fi
 +
 
 +
#    Set up for GotCloud
 +
gc=/gotcloud.mnt
 +
if [ ! -r $gc/release_version.txt ]; then
 +
   mkdir -p $gc
 +
   mount /dev/xvdg $gc
 +
   if [ -d $gc/gotcloud.ref ]; then
 
     echo "#######################################################"
 
     echo "#######################################################"
−
     echo "#  GotCloud is not set up on /gotcloud"
+
     echo "#  GotCloud is set up on $gc"
 
     echo "#######################################################"
 
     echo "#######################################################"
 
   fi
 
   fi
−
+
fi
−
  #    Setup 1000g access by s3fs
+
 
−
  usermod -aG fuse $USER
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#    Set up access to S3 storage as normal filesystem
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  echo 'AKIAIW5TQEUWZ3YCZF2Q:ft1eJa3WGzNE8iitNlbA08x/G8iMqkMIkJjFCIGf' > /etc/$FILES3
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echo "${AWSACCESSKEYID}:$AWSSECRETACCESSKEY" > $FILES3
−
  chown root.root /etc/$FILES3
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chown root.root $FILES3
−
  chmod 640 /etc/$FILES3
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chmod 640 $FILES3
−
  mkdir -p $THOUSANDG
+
 
 +
usermod -aG fuse $USER
 +
 
 +
#    Setup 1000genomes
 +
mkdir -p $THOUSANDG
 +
if [ ! -r $THOUSANDG/release ]; then
 
   chown $USER.$USER $THOUSANDG
 
   chown $USER.$USER $THOUSANDG
−
  #  It is tempting to use caching with  -o use_cache=/tmp 1000genomes
  −
  #  But s3fs cache is exceedingly dumb and does not use a least recently used
  −
  #  mechanism -- which will guarantee your root volume will fill up
   
   /usr/local/bin/s3fs -o allow_other 1000genomes $THOUSANDG > $S3ERR 2>&1
 
   /usr/local/bin/s3fs -o allow_other 1000genomes $THOUSANDG > $S3ERR 2>&1
 
   if [ ! -r $THOUSANDG/alignment.index ]; then
 
   if [ ! -r $THOUSANDG/alignment.index ]; then
−
    echo "#######################################################" >> $S3ERR
  −
    echo "#  1000genomes is not set up on $THOUSANDG" >> $S3ERR
  −
    echo "#######################################################" >> $S3ERR
  −
  fi
  −
  df -h
  −
  −
  #  Make sure we have a swap file
  −
  a=`swapon -s | grep -v Filename'
  −
  if [ "$a" = "" ]; then
   
     echo "#######################################################"
 
     echo "#######################################################"
−
     echo "#  You have no SWAP file set up"
+
     echo "#  1000genomes is not set up on $THOUSANDG"
−
    echo "#"
+
     echo "#   See S3FS errors in $S3ERR"
−
    echo "#  swap=/mnt/swapfile"
  −
    echo "#  sudo dd if=/dev/zero of=$swap bs=1073741824 count=20"
  −
     echo "# sudo chown root:root $swap"
  −
    echo "#  sudo mkswap $swap"
  −
    echo "#  sudo chmod 0600 $swap"
  −
    echo "#  sudo swapon $swap"
  −
    echo "#"
  −
    echo "#  If need be, add to /etc/fstab"
  −
    echo "#  echo "$swap  none swap sw  0  0" >> /etc/fstab"
   
     echo "#######################################################"
 
     echo "#######################################################"
 
   fi
 
   fi
 +
  df -h
 +
fi
 +
exit 0
   −
  exit 0
   
</code>
 
</code>
  
Terry Gliedt
283

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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/7516"

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