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$ vagrant ssh
Welcome to Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-39-generic x86_64)

 * Documentation:  https://help.ubuntu.com/

  System information as of Sun Dec 14 18:06:00 UTC 2014

  System load:  0.37              Processes:           100
  Usage of /:   2.7% of 39.34GB   Users logged in:     0
  Memory usage: 10%               IP address for eth0: 10.0.2.15
  Swap usage:   0%

  Graph this data and manage this system at:
    https://landscape.canonical.com/

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0 packages can be updated.
0 updates are security updates.


vagrant@vagrant-ubuntu-trusty-64:~$ ls /vagrant/
files                              smrtanalysis-patch_2.3.0.140936.p1.run
manifests                          smrtanalysis-patch_2.3.0.140936.p1.run.md5
smrtanalysis_2.3.0.140936.run      Vagrantfile
smrtanalysis_2.3.0.140936.run.md5
vagrant@vagrant-ubuntu-trusty-64:~$ bash /vagrant/smrtanalysis_2.3.0.140936.run --help
Usage: smrtanalysis_2.3.0.140936.run [--help] [--rootdir dir] \
               [--skip-extract|--no-extract] [--extract-only] \
               [--update] \
               [-p|--patchfile patchfile] \
               [-a|--addonfile addonile] \
               [--start-origcmd args... --end-origcmd] \
               [--otherargs] \
               [-- thisprog_args... [-- subprog1_args... [subprog2_args...]]]
         --rootdir       -- smrtanalysis root directory (default: ./smrtanalysis)
         --skip-extract   -- skip the tarball extraction (use previous extract)
         --no-extract     -- same as --skip-extract
         --extract-only   -- only extract the tarball, do not invoke
                            installer or upgrader
         --update         -- update from an existing install (internal option
                            only)
         --patchfile      -- patch file to apply during install/upgrade
         --addonfile      -- addon file to apply during install/upgrade
         --start-origcmd  -- original args to parent program, until 
                             until --end-origcmd arg
         --otherargs      -- unrecognized args passed to subprogs until
         -- args...       -- force args to be handled by this program
         -- -- args...    -- force args to be handled by this subprog1 
                             (first level subprog)
         -- -- -- args... -- force args to be handled by this subprog2 
                             (second level subprog)
                             recognized
         --help           -- print this usage
         -- --help        -- print this usage
         --helpall        -- print this usage and usage of subprogs

  at: 160 /vagrant/smrtanalysis_2.3.0.140936.run
vagrant@vagrant-ubuntu-trusty-64:~$ bash /vagrant/smrtanalysis_2.3.0.140936.run --rootdir /tmp --patchfile /vagrant/smrtanalysis-patch_2.3.0.140936.p1.run --extract-only
Starting smrtanalysis_2.3.0.140936 self-extraction...
Creating install directory (/tmp/install/smrtanalysis_2.3.0.140936)...
Extracting smrtanalysis_2.3.0.140936...
Starting smrtanalysis-patch_2.3.0.140936.p1.142411_linux_x86_64_libc-2.5_centos-53 self-extraction...
Creating install directory (/tmp/install/smrtanalysis-patch_2.3.0.140936.p1.142411_linux_x86_64_libc-2.5_centos-53)...
Extracting smrtanalysis-patch_2.3.0.140936.p1.142411_linux_x86_64_libc-2.5_centos-53...
Invoking smrtanalysis-patch_2.3.0.140936.p1.142411_linux_x86_64_libc-2.5_centos-53 installer...
Checking existing version number...
Copying prerun patchfiles...
Skipping smrtanalysis_2.3.0.140936 installer...
vagrant@vagrant-ubuntu-trusty-64:~$ ls /tmp/
install  vagrant-puppet-3
vagrant@vagrant-ubuntu-trusty-64:~$ ls /tmp/install/smrtanalysis
smrtanalysis_2.3.0.140936/
smrtanalysis-patch_2.3.0.140936.p1.142411_linux_x86_64_libc-2.5_centos-53/
vagrant@vagrant-ubuntu-trusty-64:~$ ls /tmp/install/smrtanalysis_2.3.0.140936/
admin/         common/        installerdeps/ misclibs/      smrtcmds/
analysis/      doc/           licenses/      postinstall/   support/
bin/           etc/           miscdeps/      redist/        
vagrant@vagrant-ubuntu-trusty-64:~$ file /tmp/install/smrtanalysis_2.3.0.140936/analysis/bin/pbdagcon
/tmp/install/smrtanalysis_2.3.0.140936/analysis/bin/pbdagcon: ELF 64-bit LSB  executable, x86-64, version 1 (SYSV), statically linked, for GNU/Linux 2.6.9, not stripped
vagrant@vagrant-ubuntu-trusty-64:~$ /tmp/install/smrtanalysis_2.3.0.140936/analysis/bin/pbdagcon --help
Usage: /tmp/install/smrtanalysis_2.3.0.140936/analysis/bin/pbdagcon [options] <input>

PacBio read-on-read error correction via consensus:
  -h [ --help ]                  Display this help
  -v [ --verbose ]               Increase logging verbosity
  -a [ --align ]                 Align sequences before adding to consensus
  -t [ --trim ] arg (=50)        Trim alignment by N bases on either side
  -m [ --min-length ] arg (=500) Filter both alignments and corrected reads 
                                 less than length
  -c [ --min-coverage ] arg (=8) Minimum coverage required to correct
  -j [ --threads ] arg           Number of consensus threads to use
  -r [ --rbuf ] arg (=30)        Size of the read buffer
  -w [ --wbuf ] arg (=30)        Size of the write buffer
  --input arg (=-)               Input (flag is optional)

vagrant@vagrant-ubuntu-trusty-64:~$