Installing SMRTanalysis package

[rhall]

Sorry, I notice that you are using SUSE. SMRTanalysis is only distributed for Ubuntu 10.04 and Centos 5.6. While Ubuntu is SUSE based getting SMRTanalysis to work will likely prove futile given the version differences for things like glibc. Unfortunately, given the complexity of the system, building from source on different Linux distributions is not an option. Depending on what you have planned there are three options:
1. Install Ubuntu 10.04 - Not generally practical, but the best option if you intend using SMRTanalysis a lot, or installing the web server for other people to use.
2. Install Ubuntu 10.04 (the server version has the smallest footprint) in a virtual machine (VM) that runs on your SUSE system.
This is probably the best option, it will give good performance, but the VM will likely take up a lot of disk space.
For setting up SUSE as a VM host:

http://doc.opensuse.org/documentation/html/openSUSE/opensuse-kvm/book.kvm.html

Or.

http://www.oracle.com/technetwork/server-storage/virtualbox/downloads/index.html

I would highly recommend virtualbox, it is very easy to use.
3. If you only want to try SMRTanalysis and are not going to do any heavy computation, or simply as a test to see if you want to go to the effort of installing it in a VM then the Amazon AMI route is very easy, but has a cost associated with it.

[GenoMax]

Hi rhall,

Thanks for your reply. After I source setup.sh, it displayed me correct python version. However, when I tried to run smrtpipe.py, I got following errors

ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /data1/smartanalysis/analysis/lib/python2.7/matplotlib-1.0.1-py2.7-linux-x86_64.egg/matplotlib/ft2font.so)

Do I need to install some extra modules or update paths or source other files?

Thanks

Stepping out of my comfort zone (I am not a sys admin) .. Is your LD_LIBRARY_PATH variable set correctly? Do you have multiple versions of "libstdc++.so.6" in /usr/lib?

On a local cluster with a working install of SMRTanalysis 1.4.0 there is only one "libstdc++.so.6" and the latest I see is GLIBCXX_3.4.8, if I do

strings /usr/lib/libstdc++.so.6 | grep GLIBC

How about

strings /opt/smrtanalysis-1.4.0/analysis/lib/python2.7/matplotlib-1.0.1-py2.7-linux-x86_64.egg/matplotlib/ft2font.so | grep GLIBC

[sagarutturkar]

Hi rhall,

Thanks for your reply. After I source setup.sh, it displayed me correct python version. However, when I tried to run smrtpipe.py, I got following errors

Traceback (most recent call last):
  File "/data1/smrtanalysis-1.4.0/analysis/bin/smrtpipe.py", line 5, in <module>
    pkg_resources.run_script('pbpy==0.1', 'smrtpipe.py')
  File "build/bdist.linux-i686/egg/pkg_resources.py", line 489, in run_script
    keys.append(dist.key)
  File "build/bdist.linux-i686/egg/pkg_resources.py", line 1207, in run_script
    def __init__(self,module):
  File "/data1/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/EGG-INFO/scripts/smrtpipe.py", line 11, in <module>
    from pbpy.smrtpipe.SmrtPipeMain import SmrtPipeMain, _sanityCheck
  File "/data1/smartanalysis/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/SmrtPipeMain.py", line 22, in <module>
    from pbpy.smrtpipe.engine.SmrtCloud import SmrtCloudWorkflow
  File "/data1/smartanalysis/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtCloud.py", line 9, in <module>
    from pbpy.smrtpipe.engine.SmrtPipeWorkflow import SmrtPipeWorkflow
  File "/data1/smartanalysis/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtPipeWorkflow.py", line 35, in <module>
    from pbpy.smrtpipe.engine.SmrtDAG import SMRTDAG
  File "/data1/smartanalysis/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtDAG.py", line 25, in <module>
    from pbpy.plot.PlotHelpers import makeHBarPlotPng
  File "/data1/smartanalysis/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/plot/PlotHelpers.py", line 10, in <module>
    import matplotlib.pyplot as plt
  File "/data1/smartanalysis/analysis/lib/python2.7/matplotlib-1.0.1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 23, in <module>
    from matplotlib.figure import Figure, figaspect
  File "/data1/smartanalysis/analysis/lib/python2.7/matplotlib-1.0.1-py2.7-linux-x86_64.egg/matplotlib/figure.py", line 18, in <module>
    from axes import Axes, SubplotBase, subplot_class_factory
  File "/data1/smartanalysis/analysis/lib/python2.7/matplotlib-1.0.1-py2.7-linux-x86_64.egg/matplotlib/axes.py", line 14, in <module>
    import matplotlib.axis as maxis
  File "/data1/smartanalysis/analysis/lib/python2.7/matplotlib-1.0.1-py2.7-linux-x86_64.egg/matplotlib/axis.py", line 10, in <module>
    import matplotlib.font_manager as font_manager
  File "/data1/smartanalysis/analysis/lib/python2.7/matplotlib-1.0.1-py2.7-linux-x86_64.egg/matplotlib/font_manager.py", line 52, in <module>
    from matplotlib import ft2font
ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /data1/smartanalysis/analysis/lib/python2.7/matplotlib-1.0.1-py2.7-linux-x86_64.egg/matplotlib/ft2font.so)

Do I need to install some extra modules or update paths or source other files?

Thanks

[rhall]

The bundled python is required for things to work. Try:

source /opt/smrtanalysis-1.4.0/etc/setup.sh

Then:

which python

Should return:

/opt/smrtanalysis-1.4.0/redist/python2.7/bin/python

[sagarutturkar]

Hi,

I am trying to install SMRTanalysis package from pacbio on SUSE Linux server.

1. Edited the setup script (/opt/smrtanalysis-1.4.0/etc/setup.sh) to match our installation location.
2. Performed fresh installation with configure_smrtanalysis.sh

Then run the command '/smartanalysis/analysis/bin/smrtpipe.py' and got an error message as below:

Traceback (most recent call last):
File "/data1/smartanalysis/analysis/bin/smrtpipe.py", line 4, in <module>
import pkg_resources
File "/usr/local/python2.7/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 2803, in <module>
working_set.require(__requires__)
File "/usr/local/python2.7/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 696, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/local/python2.7/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 594, in resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: pbpy==0.1

Its some errors related to python. The current python path its searching for is (/usr/local/python2.7/) which is our local python install. I know SMRTanalysis have python bundled under folder (smartanalysis/analysis/lib/python2.7). But it always search in local python directory and throws error.

I have setup the path for "SEYMOUR_HOME" in setup.sh. Any suggestions regarding this?