Hi,

installing tool dependency package_pybamtools_0_0_2 as well as package_pybamparser_0_0_1 cause below mansion errors.

Following the tool_dependencies.xml file:

<action type="shell_command">hg clone -r ba0341816b15fff5e0a554658d6579a60e1b12b1 https://bitbucket.org/dan/pybamtools pyBamTools</action>
<action type="make_directory">$INSTALL_DIR/lib/python</action>
<action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR</action>

I can download this package and manually compile it without errors under Galaxy environments.

Question is what are sources of these errors and how to solve them using standard Galaxy installation procedure?

After googling this errors there were mentions that it can be due to deprecated package `distribute' in new version of python and it is better to use `setuptools'.

It is also described in pybamtools sources and after small modification to use `setuptools' in setup.py script it is also manually compiled without problems.

Thanx,

Nikolaos

Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz

Extracting in /tmp/tmpDIcsTL

Now working in /tmp/tmpDIcsTL/distribute-0.6.38

Building a Distribute egg in /home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools

Traceback (most recent call last):

File "setup.py", line 248, in <module>

scripts = scripts,

File "/home/galaxy/python27/python/2.7.9/lib/python2.7/distutils/core.py", line 111, in setup

_setup_distribution = dist = klass(attrs)

File "/tmp/tmpDIcsTL/distribute-0.6.38/setuptools/dist.py", line 225, in __init__

_Distribution.__init__(self,attrs)

File "/home/galaxy/python27/python/2.7.9/lib/python2.7/distutils/dist.py", line 287, in __init__

self.finalize_options()

File "/tmp/tmpDIcsTL/distribute-0.6.38/setuptools/dist.py", line 257, in finalize_options

ep.require(installer=self.fetch_build_egg)

File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2027, in require

working_set.resolve(self.dist.requires(self.extras),env,installer))

File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2237, in requires

dm = self._dep_map

File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2466, in _dep_map

self.__dep_map = self._compute_dependencies()

File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2499, in _compute_dependencies

common = frozenset(reqs_for_extra(None))

File "/tmp/tmpDIcsTL/distribute-0.6.38/pkg_resources.py", line 2496, in reqs_for_extra

if req.marker_fn(override={'extra':extra}):

File "/tmp/tmpDIcsTL/distribute-0.6.38/_markerlib/markers.py", line 109, in marker_fn

return eval(compiled_marker, environment)

File "<environment marker>", line 1, in <module>

NameError: name 'sys_platform' is not defined

/home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools/distribute-0.6.38-py2.7.egg

Traceback (most recent call last):

File "setup.py", line 9, in <module>

use_setuptools()

File "/home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools/distribute_setup.py", line 152, in use_setuptools

return _do_download(version, download_base, to_dir, download_delay)

File "/home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools/distribute_setup.py", line 132, in _do_download

_build_egg(egg, tarball, to_dir)

File "/home/galaxy/galaxy/database/tmp/tmp-toolshed-mtdFbEf6k/pyBamTools/distribute_setup.py", line 123, in _build_egg

raise IOError('Could not build the egg.')

IOError: Could not build the egg.