Question: Can't get Galaxy to run on CentOS 7.0.1406 (Core)
1
gravatar for pstew
3.8 years ago by
pstew40
pstew40 wrote:

I'd say I'm an intermediate Linux user. I'm trying to get Galaxy setup on a new install of CentOS. Python 2.7 is installed. Following the instructions at https://wiki.galaxyproject.org/Admin/GetGalaxy .Things start initializing just fine when I run sh run.sh, but then I hit this error: 

<snip>

Initializing tool-data/twobit.loc from twobit.loc.sample
Initializing static/welcome.html from welcome.html.sample
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg
Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-u           cs4.egg
Fetched http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7.           2-py2.7.egg
Fetched http://eggs.galaxyproject.org/NoseHTML/NoseHTML-0.4.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/pexpect/pexpect-2.4-py2.7.egg
Fetched http://eggs.galaxyproject.org/PasteDeploy/PasteDeploy-1.5.0-py2.7.egg
Fetched http://eggs.galaxyproject.org/WebHelpers/WebHelpers-1.3-py2.7.egg
Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 46, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 347, in re           solve
    egg.resolve()
  File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 197, in re           solve
    return self.version_conflict( e.args[0], e.args[1] )
  File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 228, in ve           rsion_conflict
    r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.           fetch )
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 626, in resolve
    raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: Beaker==1.4
Fetch failed.
Traceback (most recent call last):
  File "./scripts/paster.py", line 29, in <module>
    pkg_resources.require( "Paste" )
  File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 416, in re           quire
    raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
galaxy.eggs.EggNotFetchable: ['Paste']

I Googled the problem, and it was suggested that someone having similar issues follow the instructions at https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer and try using a virtualenv which apparently gives you a clean slate to work on with Python. I did:

wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py

followed by

/usr/bin/python2.7 virtualenv.py --no-site-packages galaxy_env

and get the following:

New python executable in galaxy_env/bin/python2.7
Also creating executable in galaxy_env/bin/python
Installing setuptools.....................
  Complete output from command /home/stewarpa/galaxy-dist/gal...on2.7 -c "#!pyth           on
\"\"\"Bootstrap setuptoo...

 


" --always-copy -U setuptools:
  Downloading http://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11           -py2.7.egg
Traceback (most recent call last):
  File "<string>", line 278, in <module>
  File "<string>", line 210, in main
  File "<string>", line 158, in download_setuptools
  File "/usr/lib64/python2.7/urllib2.py", line 127, in urlopen
    return _opener.open(url, data, timeout)
  File "/usr/lib64/python2.7/urllib2.py", line 404, in open
    response = self._open(req, data)
  File "/usr/lib64/python2.7/urllib2.py", line 422, in _open
    '_open', req)
  File "/usr/lib64/python2.7/urllib2.py", line 382, in _call_chain
    result = func(*args)
  File "/usr/lib64/python2.7/urllib2.py", line 1216, in http_open
    return self.do_open(httplib.HTTPConnection, req)
  File "/usr/lib64/python2.7/urllib2.py", line 1186, in do_open
    raise URLError(err)
urllib2.URLError: <urlopen error [Errno -2] Name or service not known>
----------------------------------------
...Installing setuptools...done.
Traceback (most recent call last):
  File "virtualenv.py", line 1649, in <module>
    main()
  File "virtualenv.py", line 558, in main
    prompt=options.prompt)
  File "virtualenv.py", line 654, in create_environment
    install_setuptools(py_executable, unzip=unzip_setuptools)
  File "virtualenv.py", line 384, in install_setuptools
    _install_req(py_executable, unzip)
  File "virtualenv.py", line 360, in _install_req
    cwd=cwd)
  File "virtualenv.py", line 624, in call_subprocess
    % (cmd_desc, proc.returncode))
OSError: Command /home/stewarpa/galaxy-dist/gal...on2.7 -c "#!python
\"\"\"Bootstrap setuptoo...

 


" --always-copy -U setuptools failed with error code 1

I've got no idea what to do from here. Any help would be much appreciated.

 

 

software error galaxy • 3.0k views
ADD COMMENTlink modified 3.4 years ago by skx00010 • written 3.8 years ago by pstew40
2

Try deleting your eggs folder and then running  the fetch directly (make sure to run it on Python 2.7)

python ./scripts/fetch_eggs.py
ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Martin Čech ♦♦ 4.8k

I deleted all eggs in ./eggs/, ran python ./scripts/fetch_eggs.py and got the following:

Traceback (most recent call last):
  File "./scripts/fetch_eggs.py", line 46, in <module>
    c.resolve() # Only fetch eggs required by the config
  File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 347, in resolve
    egg.resolve()
  File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 197, in resolve
    return self.version_conflict( e.args[0], e.args[1] )
  File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 228, in version_conflict
    r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch )
  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 626, in resolve
    raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: Mako==0.4.1

Mako was one of the eggs that I deleted that was in the folder if that's any help. Also, I seem to be getting a lot of timeouts when installing other things unrelated to galaxy with yum. Could connectivity be an issue?

 

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by pstew40
2

Yep, as Bjoern states below it looks like it. It would be next area to explore.

ADD REPLYlink written 3.8 years ago by Martin Čech ♦♦ 4.8k

It looks like it's a connection issue. I can keep rerunning  python ./scripts/fetch_eggs.py and get a few extra eggs each time, but eventually it will timeout and error on me. I've been running this manually all day. Is there an easy way to manually download all of these at once using wget or other so I can just start the server? Thanks!

 

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by pstew40
3
gravatar for Bjoern Gruening
3.8 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

this all sounds like you have no or only partially internet connection. Can you check if you have a stable connection and can download files?

Ciao,

Bjoern

ADD COMMENTlink written 3.8 years ago by Bjoern Gruening5.1k

Thanks, this is what I figured. As I mentioned above, I can keep rerunning  python ./scripts/fetch_eggs.py and get a few extra eggs each time, but eventually it will timeout and error on me. I've been running this manually all day. Is there an easy way to manually download all of these at once using wget or other so I can just start the server? Thank you!

ADD REPLYlink written 3.8 years ago by pstew40

This sounds really strange, but you can always run the fetch script in a for loop :)

ADD REPLYlink written 3.4 years ago by Bjoern Gruening5.1k
3
gravatar for Martin Čech
3.8 years ago by
Martin Čech ♦♦ 4.8k
United States
Martin Čech ♦♦ 4.8k wrote:

I found a possible solution to your problem in our wiki:

https://wiki.galaxyproject.org/Admin/Config/Eggs

see the If your Galaxy server does not have Internet access section

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Martin Čech ♦♦ 4.8k

Great, thank you! Hopefully I can use this as a temporary fix. Our IT people are looking into the machine's connectivity issues (there have been intermittent problems in the building). 

ADD REPLYlink written 3.8 years ago by pstew40

After numerous attempts, it looks like I'm down to simplejson failing a fetch from 

python ./scripts/fetch_eggs.py

I then tried taking your advice (following the instructions for  If your Galaxy server does not have Internet access ) using a different machine with a working version of Galaxy, but I get the following message after running the .py file that downloads and zips the eggs:

<snip> 
Fetched http://eggs.galaxyproject.org/anyjson/anyjson-0.3.3-py2.7.egg
Fetched http://eggs.galaxyproject.org/WebError/WebError-0.8a-py2.7.egg
Fetched http://eggs.galaxyproject.org/twill/twill-0.9-py2.7.egg

Failed:
PyRods
simplejson

I've repeated the above numerous times (running on a different machine with Galaxy and internet) and it always fails on these two eggs. Can I manually download these eggs and put them in my eggs/ directory in the machine I'd like galaxy running on? Do you have any other suggestions for me? Thank you!

 

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by pstew40

Good news everybody!

simplejson should not be used anywhere in Galaxy anymore (is replaced) and PyRods you only need when planning to use iRods, which would be pretty rare (plus it is experimental feature)

Try starting Galaxy, it should work well. :)

----------------------- edit:
simplejson might be requirement of some of the other eggs so I would advise to find the egg for the corresponding architecture here: http://eggs.galaxyproject.org/simplejson/ and download it manually

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Martin Čech ♦♦ 4.8k
1

EDIT: Copying the egg to /eggs worked like a charm. Galaxy runs now. Hurray! Thanks for your help and patience.

--------------------------------------

Do I just need to download the json.egg and put it in the /eggs directory, or do I need to download it and scramble it to install it? Trying to get it from the internet on the original machine with connection issues sometimes times out, but sometimes I'll get the following:

python scripts/scramble.py -e simplejson
fetch_one(): Trying to fetch:
  http://eggs.galaxyproject.org/simplejson/simplejson-2.1.1.tar.gz
fetch_one(): Fetched to:
  /home/stewarpa/galaxy-dist/scripts/scramble/archives/simplejson-2.1.1.tar.gz
unpack_source(): Removing old build directory at:
  /home/stewarpa/galaxy-dist/scripts/scramble/build/py2.7/simplejson
unpack_source(): Unpacked to:
  /home/stewarpa/galaxy-dist/scripts/scramble/build/py2.7/simplejson
copy_build_script(): Using build script /home/stewarpa/galaxy-dist/scripts/scramble/scripts/generic.py
run_scramble_script(): Beginning build
run_scramble_script(): Executing in /home/stewarpa/galaxy-dist/scripts/scramble/build/py2.7/simplejson:
  /usr/bin/python scramble.py
running egg_info
writing simplejson.egg-info/PKG-INFO
writing top-level names to simplejson.egg-info/top_level.txt
writing dependency_links to simplejson.egg-info/dependency_links.txt
reading manifest file 'simplejson.egg-info/SOURCES.txt'
writing manifest file 'simplejson.egg-info/SOURCES.txt'
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/simplejson
copying simplejson/__init__.py -> build/lib.linux-x86_64-2.7/simplejson
copying simplejson/decoder.py -> build/lib.linux-x86_64-2.7/simplejson
copying simplejson/encoder.py -> build/lib.linux-x86_64-2.7/simplejson
copying simplejson/ordered_dict.py -> build/lib.linux-x86_64-2.7/simplejson
copying simplejson/scanner.py -> build/lib.linux-x86_64-2.7/simplejson
copying simplejson/tool.py -> build/lib.linux-x86_64-2.7/simplejson
creating build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/__init__.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_check_circular.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_decimal.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_decode.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_default.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_dump.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_encode_basestring_ascii.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_encode_for_html.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_fail.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_float.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_indent.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_pass1.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_pass2.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_pass3.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_recursion.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_scanstring.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_separators.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_speedups.py -> build/lib.linux-x86_64-2.7/simplejson/tests
copying simplejson/tests/test_unicode.py -> build/lib.linux-x86_64-2.7/simplejson/tests
running build_ext
building 'simplejson._speedups' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/simplejson
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -c simplejson/_speedups.c -o build/temp.linux-x86_64-2.7/simplejson/_speedups.o
gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/simplejson/_speedups.o -L/usr/lib64 -lpython2.7 -o build/lib.linux-x86_64-2.7/simplejson/_speedups.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/simplejson
copying build/lib.linux-x86_64-2.7/simplejson/__init__.py -> build/bdist.linux-x86_64/egg/simplejson
copying build/lib.linux-x86_64-2.7/simplejson/decoder.py -> build/bdist.linux-x86_64/egg/simplejson
copying build/lib.linux-x86_64-2.7/simplejson/encoder.py -> build/bdist.linux-x86_64/egg/simplejson
copying build/lib.linux-x86_64-2.7/simplejson/ordered_dict.py -> build/bdist.linux-x86_64/egg/simplejson
copying build/lib.linux-x86_64-2.7/simplejson/scanner.py -> build/bdist.linux-x86_64/egg/simplejson
copying build/lib.linux-x86_64-2.7/simplejson/tool.py -> build/bdist.linux-x86_64/egg/simplejson
creating build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/__init__.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_check_circular.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_decimal.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_decode.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_default.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_dump.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_encode_basestring_ascii.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_encode_for_html.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_fail.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_float.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_indent.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_pass1.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_pass2.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_pass3.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_recursion.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_scanstring.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_separators.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_speedups.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/tests/test_unicode.py -> build/bdist.linux-x86_64/egg/simplejson/tests
copying build/lib.linux-x86_64-2.7/simplejson/_speedups.so -> build/bdist.linux-x86_64/egg/simplejson
byte-compiling build/bdist.linux-x86_64/egg/simplejson/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/decoder.py to decoder.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/encoder.py to encoder.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/ordered_dict.py to ordered_dict.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/scanner.py to scanner.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tool.py to tool.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_check_circular.py to test_check_circular.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_decimal.py to test_decimal.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_decode.py to test_decode.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_default.py to test_default.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_dump.py to test_dump.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_encode_basestring_ascii.py to test_encode_basestring_ascii.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_encode_for_html.py to test_encode_for_html.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_fail.py to test_fail.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_float.py to test_float.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_indent.py to test_indent.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_pass1.py to test_pass1.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_pass2.py to test_pass2.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_pass3.py to test_pass3.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_recursion.py to test_recursion.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_scanstring.py to test_scanstring.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_separators.py to test_separators.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_speedups.py to test_speedups.pyc
byte-compiling build/bdist.linux-x86_64/egg/simplejson/tests/test_unicode.py to test_unicode.pyc
creating stub loader for simplejson/_speedups.so
byte-compiling build/bdist.linux-x86_64/egg/simplejson/_speedups.py to _speedups.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying simplejson.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying simplejson.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying simplejson.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying simplejson.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying simplejson.egg-info/zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Traceback (most recent call last):
  File "scripts/scramble.py", line 50, in <module>
    egg.scramble()
  File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in scramble
    raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n  %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) )
galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for simplejson did not appear to fail, but no egg found to copy from expected path:
  /home/stewarpa/galaxy-dist/scripts/scramble/build/py2.7/simplejson/dist/simplejson-2.1.1-py2.7.egg

Any idea why it can't find it? When I look in 

/home/stewarpa/galaxy-dist/scripts/scramble/build/py2.7/simplejson/dist/

I see 

simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg

so maybe it's looking for the wrong file? Can I copy or install this egg directly? Thanks!

 

 

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by pstew40
0
gravatar for skx0001
3.4 years ago by
skx00010
skx00010 wrote:

I faced the same problem on CentOS 7.

There is no compiled egg at http://eggs.galaxyproject.org/PyRods/, only exits PyRods-3.2.4.tar.gz.

And galaxy script tries fetching simplejson-2.1.1-py2.7.egg while there are files named like simplejson-2.1.1-py2.7-linux-XXXXXX.egg.

 

Are these two eggs necessary to galaxy?

 

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by skx00010
1

Our building's internet was having issues. IT replaced some switches, and I've since moved to a wired connection instead of wireless. It built and ran just fine after this. Try following these instructions: https://wiki.galaxyproject.org/Admin/Config/Eggs .

ADD REPLYlink written 3.4 years ago by pstew40
0
gravatar for skx0001
3.4 years ago by
skx00010
skx00010 wrote:

run.sh works after i did the following jobs,

 

install gcc, gcc-c++, python-devel, unzip

install python-pip from  https://bootstrap.pypa.io/get-pip.py

install pbr-0.10.8, pip-6.0.8 from https://pypi.python.org/packages/


 

--

CentOS 7 ships with python-2.7.5.  I believe most galaxy environments might use more recent python version.

I guess run.sh will compile eggs if it cannot download eggs from egg online repository. If building dependencies are missing, run.sh will fail.  Is it correct?


 

ADD COMMENTlink written 3.4 years ago by skx00010
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