June 2016 - galaxy-dev - lists.galaxyproject.org

LDAP authentification
by Durdevic, Marija 03 Jun '16

03 Jun '16

Can someone please be so kind to post auth_conf.xml file with all changes. I am trying to setup it, but unsuccessfully. Thanks in advance. Regards, Marija Mag. Marija Đurđević Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.djurdjevic(a)medunigraz.at Email: marija.djurdjevic(a)klinikum-graz.at Web: https://zmf.medunigraz.at/

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June Galaxy News: Register for GCC2016 by June 4, new papers, openings, directories, ...
by Dave Clements 01 Jun '16

01 Jun '16

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Deeptools installation fails because of missing python module(setuptools)
by Tobias Zimmermann 01 Jun '16

01 Jun '16

Hello, I'm having a problem with the installation of the "deeptools_bam_compare" tool (Revision: d5d57b40b29a). The installation of the requirements (package_python_2_7_deeptools_2_2_2) fails. The command which fails is the following (stderr output is located in /ceph/galaxy/tool_dependencys/deepTools/2.2.2/iuc/package_python_2_7_deeptools_2_2_2/0e67aa094608/INSTALLATION.log): ... easy_install --no-deps --install-dir /galaxy/tool_dependencys/deepTools/2.2.2/iuc/package_python_2_7_deeptools_2_2_2/0e67aa094608 --script-dir /galaxy/tool_dependencys/deepTools/2.2.2/iuc/package_python_2_7_deeptools_2_2_2/0e67aa094608/bin deeptools_2.2.2_src_all.tar.gz STDERR Traceback (most recent call last): File "/usr/bin/easy_install", line 5, in <module> from pkg_resources import load_entry_point File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3084, in <module> @_call_aside File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3070, in _call_aside f(*args, **kwargs) File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3097, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master return cls._build_from_requirements(__requires__) File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in _build_from_requirements dists = ws.resolve(reqs, Environment()) File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 839, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'setuptools==3.3' distribution was not found and is required by the application ... The problem seems to be the missing / wrong version of setuptools. The next step for me was to check the missing tool dependencies error reports. All tool dependencies (deepTools, pysam, matplotlib, bx-python, scipy, pybigwig and numpy) show the same error with the missing setuptools. Only the package_python_2_7_10 dependency is installed correct. I checked the setuptools version in the python dependency (/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/setuptools/version.py) and it's version 18.2 (__version__ = '18.2'). This might be the problem here? I am using Galaxy release_15.05. Thanks, Tobias

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Intallation of deeptools fails
by Tobias Zimmermann 01 Jun '16

01 Jun '16

Hello, I'm having a problem with the installation of the "deeptools_bam_compare" tool (Revision: d5d57b40b29a). The installation of the requirements (package_python_2_7_deeptools_2_2_2) fails. The command which fails is the following (stderr output is located in /ceph/galaxy/tool_dependencys/deepTools/2.2.2/iuc/package_python_2_7_deeptools_2_2_2/0e67aa094608/INSTALLATION.log): ... easy_install --no-deps --install-dir /galaxy/tool_dependencys/deepTools/2.2.2/iuc/package_python_2_7_deeptools_2_2_2/0e67aa094608 --script-dir /galaxy/tool_dependencys/deepTools/2.2.2/iuc/package_python_2_7_deeptools_2_2_2/0e67aa094608/bin deeptools_2.2.2_src_all.tar.gz STDERR Traceback (most recent call last): File "/usr/bin/easy_install", line 5, in <module> from pkg_resources import load_entry_point File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3084, in <module> @_call_aside File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3070, in _call_aside f(*args, **kwargs) File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3097, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 653, in _build_master return cls._build_from_requirements(__requires__) File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in _build_from_requirements dists = ws.resolve(reqs, Environment()) File "/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/pkg_resources/__init__.py", line 839, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'setuptools==3.3' distribution was not found and is required by the application ... The problem seems to be the missing / wrong version of setuptools. The next step for me was to check the missing tool dependencies error reports. All tool dependencies (deepTools, pysam, matplotlib, bx-python, scipy, pybigwig and numpy) show the same error with the missing setuptools. Only the package_python_2_7_10 dependency is installed correct. I checked the setuptools version in the python dependency (/ceph/galaxy/tool_dependencys/python/2.7.10/iuc/package_python_2_7_10/0339c4a9b87b/lib/python2.7/site-packages/setuptools/version.py) and it's version 18.2 (__version__ = '18.2'). This might be the problem here? I am using Galaxy release_15.05. Thanks, Tobias

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