Docker build fails on Step 8 : RUN cd oncotator/ && python setup.py install #348

alanhoyle · 2016-04-08T20:04:06Z

I downloaded the oncotator-1.8.0.0 tar.gz, and was trying to build the docker image. It's failng at step 8 for me.

$ docker build -t oncotator .
Sending build context to Docker daemon  41.1 MB
Sending build context to Docker daemon
Step 0 : FROM python:2
 ---> 6087f74a2b3c
Step 1 : MAINTAINER Alex Ramos <aramos@broadinstitute.org>
 ---> Using cache
 ---> 4e9363437333
Step 2 : RUN apt-get update && apt-get install unzip 
 ---> Using cache
 ---> 983db98ae5c3
Step 3 : RUN pip install numpy
 ---> Using cache
 ---> aa892798b31d
Step 4 : RUN wget --no-check-certificate 'https://github.com/elephanthunter/PyVCF/archive/master.zip'
 ---> Using cache
 ---> 4cea363534eb
Step 5 : RUN unzip master.zip && cd PyVCF-master && python setup.py install && cd .. && rm -Rf PyVCF-master && rm -f master.*
 ---> Using cache
 ---> 33c9f2b86fdb
Step 6 : RUN pip install ngslib
 ---> Using cache
 ---> 545b1ac0c75a
Step 7 : ADD . /oncotator
 ---> Using cache
 ---> 0dc41deaa12f
Step 8 : RUN cd oncotator/ && python setup.py install
 ---> Running in 69ef9bb1887c
Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.15.tar.gz
Extracting in /tmp/tmpVjVGBK
Now working in /tmp/tmpVjVGBK/distribute-0.6.15
Building a Distribute egg in /oncotator
/oncotator/distribute-0.6.15-py2.7.egg
running install
running bdist_egg
running egg_info
creating Oncotator.egg-info
[.....SNIP.....] 
Installing easy_install-2.7 script to /usr/local/bin

Installed /usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg
Traceback (most recent call last):
  File "setup.py", line 142, in <module>
    'Topic :: Scientific/Engineering :: Medical Science Apps.',
  File "/usr/local/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "build/bdist.linux-x86_64/egg/setuptools/command/install.py", line 73, in run
  File "build/bdist.linux-x86_64/egg/setuptools/command/install.py", line 101, in do_egg_install
  File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 344, in run

  File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 564, in easy_install

  File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 616, in install_item

  File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 663, in process_distribution

TypeError: __init__() takes exactly 2 arguments (4 given)
2016/04/08 15:58:37 The command '/bin/sh -c cd oncotator/ && python setup.py install' returned a non-zero code: 1

The text was updated successfully, but these errors were encountered:

LeeTL1220 · 2016-04-08T21:03:52Z

I wonder if this is related to the travis failures. @lbergelson

On Fri, Apr 8, 2016 at 4:04 PM, Alan Hoyle notifications@github.com wrote:

I downloaded the oncotator-1.8.0.0 tar.gz, and was trying to build the
docker image. It's failng at step 8 for me.

$ docker build -t oncotator .
Sending build context to Docker daemon 41.1 MB
Sending build context to Docker daemon
Step 0 : FROM python:2
---> 6087f74a2b3c
Step 1 : MAINTAINER Alex Ramos aramos@broadinstitute.org
---> Using cache
---> 4e9363437333
Step 2 : RUN apt-get update && apt-get install unzip
---> Using cache
---> 983db98ae5c3
Step 3 : RUN pip install numpy
---> Using cache
---> aa892798b31d
Step 4 : RUN wget --no-check-certificate 'https://github.com/elephanthunter/PyVCF/archive/master.zip'
---> Using cache
---> 4cea363534eb
Step 5 : RUN unzip master.zip && cd PyVCF-master && python setup.py install && cd .. && rm -Rf PyVCF-master && rm -f master.*
---> Using cache
---> 33c9f2b86fdb
Step 6 : RUN pip install ngslib
---> Using cache
---> 545b1ac0c75a
Step 7 : ADD . /oncotator
---> Using cache
---> 0dc41deaa12f
Step 8 : RUN cd oncotator/ && python setup.py install
---> Running in 69ef9bb1887c
Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.15.tar.gz
Extracting in /tmp/tmpVjVGBK
Now working in /tmp/tmpVjVGBK/distribute-0.6.15
Building a Distribute egg in /oncotator
/oncotator/distribute-0.6.15-py2.7.egg
running install
running bdist_egg
running egg_info
creating Oncotator.egg-info
[.....SNIP.....]
Installing easy_install-2.7 script to /usr/local/bin

Installed /usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg
Traceback (most recent call last):
File "setup.py", line 142, in
'Topic :: Scientific/Engineering :: Medical Science Apps.',
File "/usr/local/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "build/bdist.linux-x86_64/egg/setuptools/command/install.py", line 73, in run
File "build/bdist.linux-x86_64/egg/setuptools/command/install.py", line 101, in do_egg_install
File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 344, in run

File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 564, in easy_install

File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 616, in install_item

File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 663, in process_distribution

TypeError: init() takes exactly 2 arguments (4 given)
2016/04/08 15:58:37 The command '/bin/sh -c cd oncotator/ && python setup.py install' returned a non-zero code: 1

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#348

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

lbergelson · 2016-04-08T21:24:57Z

There's something wrong with the build in general. I'm seeing the same error. If I try to install it myself.

LeeTL1220 · 2016-04-08T21:28:25Z

I'm testing it now on my machine.

On Fri, Apr 8, 2016 at 5:25 PM, Louis Bergelson notifications@github.com
wrote:

There's something wrong with the build in general. I'm seeing the same
error. If I try to install it myself.

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#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

lbergelson · 2016-04-08T21:29:06Z

It looks like removing the , at the end of setup.py line 142 seems to stop me from getting the error. I then run into a

Installed /Users/louisb/Workspace/oncotator/oncotest2/lib/python2.7/site-packages/Oncotator-v1.8.0.0-py2.7.egg
Processing dependencies for Oncotator==v1.8.0.0
Searching for pysam==0.7.5
Reading http://pypi.python.org/simple/pysam/
No local packages or download links found for pysam==0.7.5
error: Could not find suitable distribution for Requirement.parse('pysam==0.7.5')

LeeTL1220 · 2016-04-08T21:29:15Z

(installing the docker image)

On Fri, Apr 8, 2016 at 5:28 PM, Lee Lichtenstein <
lichtens@broadinstitute.org> wrote:

I'm testing it now on my machine.

On Fri, Apr 8, 2016 at 5:25 PM, Louis Bergelson notifications@github.com
wrote:

There's something wrong with the build in general. I'm seeing the same
error. If I try to install it myself.

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Reply to this email directly or view it on GitHub
#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

alanhoyle · 2016-04-08T21:29:35Z

Note that if I try to run an interactive build by running $ docker run -it --entrypoint /bin/bash 0dc41deaa12f, I get different results on the second time if I try to run the "python setup.py install" again.

(takes a while to get to it, but it's doing some cython/numpy installation along the way)

Running numpy-1.11.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-jeo0vy/numpy-1.11.0/egg-dist-tmp-3sbxNC
/tmp/easy_install-jeo0vy/numpy-1.11.0/setup.py:327: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
  warnings.warn("Unrecognized setuptools command, proceeding with "
Warning: distutils distribution has been initialized, it may be too late to add a subpackage compatTraceback (most recent call last):
  File "setup.py", line 142, in <module>
    'Topic :: Scientific/Engineering :: Medical Science Apps.',
  File "/usr/local/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/install.py", line 73, in run
    self.do_egg_install()
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/install.py", line 101, in do_egg_install
    cmd.run()
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 344, in run
    self.easy_install(spec, not self.no_deps)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 564, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 616, in install_item
    self.process_distribution(spec, dist, deps)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 668, in process_distribution
    [requirement], self.local_index, self.easy_install
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/pkg_resources.py", line 544, in resolve
    dist = best[req.key] = env.best_match(req, self, installer)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/pkg_resources.py", line 786, in best_match
    return self.obtain(req, installer) # try and download/install
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/pkg_resources.py", line 798, in obtain
    return installer(requirement)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 584, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 614, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 804, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 1081, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 1070, in run_setup
    run_setup(setup_script, args)
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/sandbox.py", line 29, in run_setup
    lambda: execfile(
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/sandbox.py", line 70, in run
    return func()
  File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/sandbox.py", line 31, in <lambda>
    {'__file__':setup_script, '__name__':'__main__'}
  File "setup.py", line 386, in <module>

  File "setup.py", line 378, in setup_package

  File "/usr/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup
    config = configuration()
  File "setup.py", line 161, in configuration

  File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
    caller_level = 2)
  File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
    caller_level = caller_level + 1)
  File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "numpy/setup.py", line 10, in configuration

  File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
    caller_level = 2)
  File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
    caller_level = caller_level + 1)
  File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 884, in _get_configuration_from_setup_py
    ('.py', 'U', 1))
  File "numpy/core/setup.py", line 13, in <module>
    NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
ImportError: No module named _build_utils.apple_accelerate

LeeTL1220 · 2016-04-08T21:30:33Z

Are you guys both on mac?

On Fri, Apr 8, 2016 at 5:29 PM, Alan Hoyle notifications@github.com wrote:

Note that if I try to run an interactive build by running $ docker run
-it --entrypoint /bin/bash 0dc41deaa12f, I get different results on the
second time if I try to run the "python setup.py install" again.

Running numpy-1.11.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-jeo0vy/numpy-1.11.0/egg-dist-tmp-3sbxNC
/tmp/easy_install-jeo0vy/numpy-1.11.0/setup.py:327: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
warnings.warn("Unrecognized setuptools command, proceeding with "
Warning: distutils distribution has been initialized, it may be too late to add a subpackage compatTraceback (most recent call last):
File "setup.py", line 142, in
'Topic :: Scientific/Engineering :: Medical Science Apps.',
File "/usr/local/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/install.py", line 73, in run
self.do_egg_install()
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/install.py", line 101, in do_egg_install
cmd.run()
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 344, in run
self.easy_install(spec, not self.no_deps)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 564, in easy_install
return self.install_item(None, spec, tmpdir, deps, True)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 616, in install_item
self.process_distribution(spec, dist, deps)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 668, in process_distribution
[requirement], self.local_index, self.easy_install
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/pkg_resources.py", line 544, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/pkg_resources.py", line 786, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/pkg_resources.py", line 798, in obtain
return installer(requirement)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 584, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 614, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 804, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 1081, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py", line 1070, in run_setup
run_setup(setup_script, args)
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/sandbox.py", line 29, in run_setup
lambda: execfile(
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/sandbox.py", line 70, in run
return func()
File "/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg/setuptools/sandbox.py", line 31, in
{'file':setup_script, 'name':'main'}
File "setup.py", line 386, in

File "setup.py", line 378, in setup_package

File "/usr/local/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "setup.py", line 161, in configuration

File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "numpy/setup.py", line 10, in configuration

File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 884, in _get_configuration_from_setup_py
('.py', 'U', 1))
File "numpy/core/setup.py", line 13, in
NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
ImportError: No module named _build_utils.apple_accelerate

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#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

lbergelson · 2016-04-08T21:30:57Z

I'm just installing locally in a venv, not running the docker build. On a mac. I assume the docker isn't running mac though?

LeeTL1220 · 2016-04-08T21:31:34Z

Docker definitely not.

On Fri, Apr 8, 2016 at 5:30 PM, Louis Bergelson notifications@github.com
wrote:

I'm just installing locally in a venv, not running the docker build. On a
mac. I assume the docker isn't running mac though?

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#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

LeeTL1220 · 2016-04-08T21:38:05Z

Boom:

Installed /usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg
Traceback (most recent call last):
  File "setup.py", line 142, in <module>
    'Topic :: Scientific/Engineering :: Medical Science Apps.',
  File "/usr/local/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in
run_commands
    self.run_command(cmd)
  File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in
run_command
    cmd_obj.run()
  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/install.py",
line 73, in run
  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/install.py",
line 101, in do_egg_install
  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 344, in run

  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 564, in easy_install

  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 616, in install_item

  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 663, in process_distribution

TypeError: __init__() takes exactly 2 arguments (4 given)

On Fri, Apr 8, 2016 at 5:31 PM, Lee Lichtenstein <
lichtens@broadinstitute.org> wrote:

Docker definitely not.

On Fri, Apr 8, 2016 at 5:30 PM, Louis Bergelson notifications@github.com
wrote:

I'm just installing locally in a venv, not running the docker build. On a
mac. I assume the docker isn't running mac though?

—
You are receiving this because you commented.
Reply to this email directly or view it on GitHub
#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

LeeTL1220 · 2016-04-08T21:38:36Z

Oddly enough CGA (Broad internal) is running the docker image without
issues related to this....

On Fri, Apr 8, 2016 at 5:37 PM, Lee Lichtenstein <
lichtens@broadinstitute.org> wrote:

Boom:
Installed
/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg
Traceback (most recent call last):
  File "setup.py", line 142, in <module>
    'Topic :: Scientific/Engineering :: Medical Science Apps.',
  File "/usr/local/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in
run_commands
    self.run_command(cmd)
  File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in
run_command
    cmd_obj.run()
  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/install.py",
line 73, in run
  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/install.py",
line 101, in do_egg_install
  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 344, in run

  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 564, in easy_install

  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 616, in install_item

  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 663, in process_distribution

TypeError: __init__() takes exactly 2 arguments (4 given)
On Fri, Apr 8, 2016 at 5:31 PM, Lee Lichtenstein <
lichtens@broadinstitute.org> wrote:

Docker definitely not.

On Fri, Apr 8, 2016 at 5:30 PM, Louis Bergelson <notifications@github.com

wrote:

I'm just installing locally in a venv, not running the docker build. On
a mac. I assume the docker isn't running mac though?

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#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

LeeTL1220 · 2016-04-08T21:39:55Z

(I just sent email to confirm that they made no changes)

On Fri, Apr 8, 2016 at 5:38 PM, Lee Lichtenstein <
lichtens@broadinstitute.org> wrote:

Oddly enough CGA (Broad internal) is running the docker image without
issues related to this....

On Fri, Apr 8, 2016 at 5:37 PM, Lee Lichtenstein <
lichtens@broadinstitute.org> wrote:
Boom:
Installed
/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg
Traceback (most recent call last):
  File "setup.py", line 142, in <module>
    'Topic :: Scientific/Engineering :: Medical Science Apps.',
  File "/usr/local/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/local/lib/python2.7/distutils/dist.py", line 953, in
run_commands
    self.run_command(cmd)
  File "/usr/local/lib/python2.7/distutils/dist.py", line 972, in
run_command
    cmd_obj.run()
  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/install.py",
line 73, in run
  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/install.py",
line 101, in do_egg_install
  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 344, in run

  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 564, in easy_install

  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 616, in install_item

  File
"/oncotator/distribute-0.6.15-py2.7.egg/setuptools/command/easy_install.py",
line 663, in process_distribution

TypeError: __init__() takes exactly 2 arguments (4 given)
On Fri, Apr 8, 2016 at 5:31 PM, Lee Lichtenstein <
lichtens@broadinstitute.org> wrote:

Docker definitely not.

On Fri, Apr 8, 2016 at 5:30 PM, Louis Bergelson <
notifications@github.com> wrote:

I'm just installing locally in a venv, not running the docker build. On
a mac. I assume the docker isn't running mac though?

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#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632
Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

alanhoyle · 2016-04-08T21:46:00Z

I'm running an older version of Docker (1.2.0) on a Centos 6.2 compute node.

LeeTL1220 · 2016-04-08T21:48:56Z

I had to upgrade docker to 1.6.x from 1.5.0 to get the docker image to
work. Are you sure that is the version you are running? That is really
old....

On Fri, Apr 8, 2016 at 5:46 PM, Alan Hoyle notifications@github.com wrote:

I'm running an older version of Docker (1.2.0) on a Centos 6.2 compute
node.

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#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

LeeTL1220 · 2016-04-08T21:56:47Z

I just had it complete successfully by changing the first line in the docker file to python:2.7.9 from python:2 ... That change will be in the next release of oncotator (coming soon)

alanhoyle · 2016-04-08T22:11:04Z

Yep, it's definitely Docker 1.2.0. The cluster is definitely in need of an update as that's apparently the latest version of Docker that supports Centos 6.2. I noticed the Docker page talking about Centos says that they support Centos 7+ https://docs.docker.com/engine/installation/linux/centos/ Guess it's time to talk to our admins....

LeeTL1220 · 2016-04-08T22:12:26Z

I think the docker image might work anyway if you change the docker file as
I said in previous comment. No guarantees, though.
On Apr 8, 2016 6:11 PM, "Alan Hoyle" notifications@github.com wrote:

Yep, it's definitely Docker 1.2.0. The cluster is definitely in need of an
update as that's apparently the latest version of Docker that supports
Centos 6.2. I noticed the Docker page talking about Centos says that they
support Centos 7+
https://docs.docker.com/engine/installation/linux/centos/ Guess it's time
to talk to our admins....

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#348 (comment)

LeeTL1220 · 2016-04-08T23:59:49Z

Also, I think these issues will go away in v1.9.x

On Fri, Apr 8, 2016 at 6:12 PM, Lee Lichtenstein <
lichtens@broadinstitute.org> wrote:

I think the docker image might work anyway if you change the docker file
as I said in previous comment. No guarantees, though.
On Apr 8, 2016 6:11 PM, "Alan Hoyle" notifications@github.com wrote:

Yep, it's definitely Docker 1.2.0. The cluster is definitely in need of
an update as that's apparently the latest version of Docker that supports
Centos 6.2. I noticed the Docker page talking about Centos says that they
support Centos 7+
https://docs.docker.com/engine/installation/linux/centos/ Guess it's
time to talk to our admins....

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#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

LeeTL1220 · 2016-04-09T02:39:26Z

@alanhoyle I believe that if v1.9.x (coming soon) does not fix your issues, then you likely do have a problem on your end.

LeeTL1220 · 2016-04-15T16:04:13Z

Closed by #344

alanhoyle · 2016-04-15T18:53:14Z

One of my co-workers made a build that works using an interactive session rather than a Dockerfile. He documented his steps and he started with the CentOs image, rather than Python2, but it shouldn't be too hard to make a Dockerfile. (there are obvious things to improve, e.g. combining the yum and pip commands, using curl and piping its output directly to tar, etc.)

Since you all are saying that 1.9.x is due soon, it might not be worth the effort to convert.

$ docker run -i -t centos /bin/bash # at the regular command line
[root@...] # imagine these prompts inside the container for the rest:  

cd /
yum -y install wget
yum -y install python-devel.x86_64
yum -y install gcc
yum -y install gcc-c++
yum -y install zlib-devel
yum -y install unzip
yum -y install bzip2
yum -y install make
wget https://github.com/broadinstitute/oncotator/archive/v1.8.0.0.tar.gz
rpm -iUvh http://dl.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-5.noarch.rpm
yum -y install python-pip
pip install bcbio-gff
pip install biopython
pip install cython
pip install nose
pip install numpy
pip install pandas
pip install shove
pip install sqlalchemy
cd /
wget https://pysam.googlecode.com/files/pysam-0.7.5.tar.gz
tar -zxvf pysam-0.7.5.tar.gz
cd pysam-0.7.5
python setup.py install
pip install python-memcached
cd /
wget https://github.com/elephanthunter/PyVCF/archive/master.zip
unzip master.zip
cd PyVCF-master/
python setup.py install
cd /
wget https://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2/download
mv download tabix-0.2.6.tar.bz2
bzip2 -d tabix-0.2.6.tar.bz2
tar -xvf tabix-0.2.6.tar
cd tabix-0.2.6
make
cp tabix /usr/bin/
yum -y install samtools
cd /
wget https://github.com/broadinstitute/oncotator/archive/v1.8.0.0.tar.gz
tar -zxvf v1.8.0.0.tar.gz
cd oncotator-1.8.0.0/
python setup.py install

LeeTL1220 · 2016-04-15T18:57:27Z

I just released 1.9.x

On Fri, Apr 15, 2016 at 2:53 PM, Alan Hoyle notifications@github.com
wrote:

One of my co-workers made a build that works using an interactive session
rather than a Dockerfile. He documented his steps and he started with the
CentOs image, rather than Python2, but it shouldn't be too hard to make a
Dockerfile. (there are obvious things to improve, e.g. combining the yum
and pip commands, using curl and piping its output directly to tar, etc.)

Since you all are saying that 1.9.x is due soon, it might not be worth the
effort to convert.

$ docker run -i -t centos /bin/bash # at the regular command line
[root@...] # imagine these prompts inside the container for the rest:
cd /
yum -y install wget
yum -y install python-devel.x86_64
yum -y install gcc
yum -y install gcc-c++
yum -y install zlib-devel
yum -y install unzip
yum -y install bzip2
yum -y install make
wget https://github.com/broadinstitute/oncotator/archive/v1.8.0.0.tar.gz
rpm -iUvh http://dl.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-5.noarch.rpm
yum -y install python-pip
pip install bcbio-gff
pip install biopython
pip install cython
pip install nose
pip install numpy
pip install pandas
pip install shove
pip install sqlalchemycd /
wget https://pysam.googlecode.com/files/pysam-0.7.5.tar.gz
tar -zxvf pysam-0.7.5.tar.gzcd pysam-0.7.5
python setup.py install
pip install python-memcachedcd /
wget https://github.com/elephanthunter/PyVCF/archive/master.zip
unzip master.zipcd PyVCF-master/
python setup.py installcd /
wget https://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2/download
mv download tabix-0.2.6.tar.bz2
bzip2 -d tabix-0.2.6.tar.bz2
tar -xvf tabix-0.2.6.tarcd tabix-0.2.6
make
cp tabix /usr/bin/
yum -y install samtoolscd /
wget https://github.com/broadinstitute/oncotator/archive/v1.8.0.0.tar.gz
tar -zxvf v1.8.0.0.tar.gzcd oncotator-1.8.0.0/
python setup.py install

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#348 (comment)

Lee Lichtenstein
Broad Institute
75 Ames Street, Room 7003EB
Cambridge, MA 02142
617 714 8632

LeeTL1220 mentioned this issue Apr 8, 2016

Issue 343 fix ex ac ds #344

Merged

LeeTL1220 closed this as completed Apr 15, 2016

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Docker build fails on Step 8 : RUN cd oncotator/ && python setup.py install #348

Docker build fails on Step 8 : RUN cd oncotator/ && python setup.py install #348

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