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

Closed alanhoyle closed 8 years ago

alanhoyle commented 8 years ago

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
LeeTL1220 commented 8 years ago

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

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/broadinstitute/oncotator/issues/348

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

lbergelson commented 8 years ago

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

LeeTL1220 commented 8 years ago

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.

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/broadinstitute/oncotator/issues/348#issuecomment-207611598

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

lbergelson commented 8 years ago

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 commented 8 years ago

(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.

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/broadinstitute/oncotator/issues/348#issuecomment-207611598

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 commented 8 years ago

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 commented 8 years ago

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

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/broadinstitute/oncotator/issues/348#issuecomment-207612836

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

lbergelson commented 8 years ago

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 commented 8 years ago

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 https://github.com/broadinstitute/oncotator/issues/348#issuecomment-207613189

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

LeeTL1220 commented 8 years ago

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 https://github.com/broadinstitute/oncotator/issues/348#issuecomment-207613189

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 commented 8 years ago

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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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 commented 8 years ago

(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?

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/broadinstitute/oncotator/issues/348#issuecomment-207613189

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 commented 8 years ago

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

LeeTL1220 commented 8 years ago

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

LeeTL1220 commented 8 years ago

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 commented 8 years ago

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 commented 8 years ago

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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LeeTL1220 commented 8 years ago

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....

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/broadinstitute/oncotator/issues/348#issuecomment-207626113

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

LeeTL1220 commented 8 years ago

@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 commented 8 years ago

Closed by #344

alanhoyle commented 8 years ago

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 commented 8 years ago

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