- galaxy-dev - lists.galaxyproject.org

The state of the MOTHUR merge?
by Peter van Heusden 03 Jun '16

03 Jun '16

PR #429 on tools-iuc contains the updated MOTHUR toolsuite for Galaxy. https://github.com/galaxyproject/tools-iuc/pull/429 It *looks* like it is ready to merge - what is still needed before it merges into tools-iuc? Thanks! Peter

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Re: [galaxy-dev] LDAP authentication
by mark fernandes (IFR) 03 Jun '16

03 Jun '16

Don't know if this helps or not but here's the link to Novell's entry on LDAP support for eDirectory https://www.novell.com/documentation/edir873/?page=/documentation/edir873/e… Mark Fernandes T: +44 (0)1603 255000 Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK www.ifr.ac.uk Facebook | Twitter | LinkedIn | YouTube The Institute of Food Research receives strategic funding from BBSRC

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atlas 3.10 IUC error
by Olivier CLAUDE 03 Jun '16

03 Jun '16

Hello again, I am truly sorry to bother everyone again but i still experience problems: This time with atlas 3.10 owned by iuc At the beginning without modifying anything, the error log was saying " mkdir : cannot create directory ATLAS/build : No such file or directory" After that I tried to modify the tool_dependencies.xml : L48 : "mkdir ATLAS/build &&" changed to "mkdir build &&" The error is "/bin/sh: 4 : cannot open /host/static_full_blas_lapack.diff: No such file" I can see it, if I go with a web browser, but I cannot download it manually nor click on it without crashing the web browser. Any idea? Thanks again, M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de médecine Pitié-Salpêtrière 91, bld de l'Hôpital - 3ème étage - Porte 305 75013 Paris - FRANCE

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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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GCC2016: Register by this Saturday; Posters & Demos posted
by Dave Clements 31 May '16

31 May '16

Hello all, Some GCC2016 <https://gcc2016.iu.edu/> news: - *On-time registration <https://gcc2016.iu.edu/registration/index.php> for GCC2016 ends this Saturday, June 4. *After that *late registration kicks in and rates go up 100%*. You don't want to pay that. (Training <http://gcc16.sched.org/overview/type/D.x+Training+-+All> has also started to fill up, so register now to get the sessions you want.) - The full conference schedule <http://gcc16.sched.org/> is now online, including talks <http://gcc16.sched.org/overview/type/E.1+Conference+-+Talks>, posters <http://gcc16.sched.org/overview/type/E.2+Conference+-+Posters> and demos <http://gcc16.sched.org/overview/type/E.3+Conference+-+Demos>. - We still have space for a limited number of posters. Please submit your ideas now <https://docs.google.com/forms/d/1BEMl2nVx-GDz-0tbOOjGvC29bVu8TE_SFgTHtLXgn8…>, before we run out of space. Hope to see you there, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Bug Found: 2 tabs in browser open to different histories confuses tools
by Ryan G 31 May '16

31 May '16

Hi all - I think I found a bug. I have two histories open in two separate tabs in Chrome. When I try to run a tool and select an item from my history, the wrong history items are displayed. Ryan

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Problem running bwa-mem
by C. Ch. 31 May '16

31 May '16

Hi all, When running bwa-mem (installed version 0.7.12.1) I get an empty result with the stderr giving the following error: [main] Version: 0.7.12-r1039 [main] CMD: bwa mem -t 1 -v 1 -I 180 localref.fa /home/galaxy/galaxy/database/files/001/dataset_1958.dat /home/galaxy/galaxy/database/files/001/dataset_1961.dat [main] Real time: 12964.149 sec; CPU: 13152.174 sec [bam_sort_core] merging from 50 files... open: No such file or directory [bam_merge_core] fail to open file /home/galaxy/galaxy/database/files/016/dataset_16712.dat.0000 But the files exist and have the .bam extension (i.e. .../016/dataset_16712.dat.000.bam). How can I solve this? Thanks, Cristian

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