- galaxy-dev - lists.galaxyproject.org

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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SFTP settings
by Durdevic, Marija 30 May '16

30 May '16

Is there anyone who manage to setup SFTP for Glaxay and that can help me please???

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PLINK 1.90 wrapper
by Jochen Bick 30 May '16

30 May '16

Hi all, I just found the plink tool in two version 1.9 and 1.7. It looks like that it has no wrapper yet? Is it possible that the owner gives a feedback about this? We are are very interested in that tool. Cheers Jochen

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