September 2011 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] use_tasked_jobs
by Chorny, Ilya 23 Sep '11

23 Sep '11

Hi Nate, We are having an issue that when use_tasked_jobs = True, the job_wrapper.user = None in drama.py. Do you know why that might be. It crashes my code. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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use_tasked_jobs and drmaa
by Chorny, Ilya 23 Sep '11

23 Sep '11

So we have some new issues with use_tasked_jobs and drama and wanted to share with the community. 1.) The task get split on the head node which will bog down the head node if multiple user submit a job which requires splitting. It would be great if we could submit that to drmaa. 2.) Can't kill the job while it's being split. 3.) Can't kill the job when it finally gets submitted to the drama. (Looks like there needs to be some logic to assign multiple drama job id's with the galalxy job ID). Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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ImportError _PyLong_AsScaledDouble
by Alex R Bigelow 23 Sep '11

23 Sep '11

Hi, I restarted my Galaxy server this morning (it was working fine before), but now I'm getting the following error: Error at initialization of module heapycTraceback (most recent call last): File "/export/home/alex/Apps/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/export/home/alex/Apps/galaxy-dist/lib/galaxy/app.py", line 78, in __init__ self.memdump = memdump.Memdump() File "/export/home/alex/Apps/galaxy-dist/lib/galaxy/util/memdump.py", line 24, in __init__ self.heapy = guppy.hpy() File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/__init__.py", line 35, in hpy return r.guppy.heapy.Use File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 44, in __getattr__ return self._share.getattr(self, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 187, in getattr d = self.getattr2(inter, cache, owner, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 202, in getattr2 x = self.getattr_package(inter, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 250, in getattr_package x = self.makeModule(x, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 310, in makeModule return Share(module, self, module.__name__, Clamp) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 176, in __init__ getattr(inter, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 44, in __getattr__ return self._share.getattr(self, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 187, in getattr d = self.getattr2(inter, cache, owner, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 204, in getattr2 x = self.getattr3(inter, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 272, in getattr3 pa = getattr(pa, at) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 44, in __getattr__ return self._share.getattr(self, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 187, in getattr d = self.getattr2(inter, cache, owner, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 202, in getattr2 x = self.getattr_package(inter, name) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/etc/Glue.py", line 239, in getattr_package x = __import__(self.makeName(name), globals(), locals()) File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/heapy/View.py", line 556, in <module> prime_builtin_types() File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/heapy/View.py", line 539, in prime_builtin_types import guppy.heapy.heapyc File "/export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/sets/__init__.py", line 3, in <module> from setsc import BitSet # base bitset type ImportError: /export/home/alex/Apps/galaxy-dist/eggs/guppy-0.1.8-py2.7-linux-x86_64-ucs2.egg/guppy/sets/setsc.so: undefined symbol: _PyLong_AsScaledDouble I think it downloaded a new package when I tried to start it; I think I may have found a relevant thread with a patch at http://aur.achlinux.org/packages.php?ID=43710 but I'm not sure how to go about applying it. Thanks, Alex Bigelow

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OpenID
by mgreenway＠uchicago.edu 23 Sep '11

23 Sep '11

Hello Galaxy Developers: I noticed a few issues with the OpendID system. The first is that attempting to log in with an OpenID not associated with a galaxy account gives a "Server Error" page. Also using Flickr as an OP gives: "Failed to begin OpenID authentication: No usable OpenID services found for http://flickr.com" I haven't looked into whether Flickr has a different OP URL or none at all. I was wondering if someone was working on these or if they had been fixed in a different version. If not then I will work on fixing them and try to make my code available for others. Thanks, Matt Greenway

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enabled user_library_import_dir but see nothing in the GUI to be able to create data libraries
by Leandro Hermida 23 Sep '11

23 Sep '11

Hi all, I've enabled the universe.wsgi feature user_library_import_dir feature and made a sub-directory with my login and put some test files there. I've also made myselfa non-admin to test and after restart the Galaxy server I see no where in the GUI where I can import data libraries?? Am I missing something? regards, Leandro

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Specifying a range of inputs?
by Timothy Wu 23 Sep '11

23 Sep '11

Hi, I'm implementing my own tools. In one tool I may have hundreds of input files. (or maybe I'm doing it wrong?) I'm copying off the tool conf xml code from the "concatenate dataset" tool. But this requires adding files one by one. Is there a quicker way in which I can just specify these files from the job number? Say I want data from job 42 to 323, something like that. I haven't attempt to run the tool yet. I'm also curious if there is a limit to how long the command can be at the shell level. I suspect the tool won't be able to run especially with each of the galaxy files is designated in the absolute path. Timothy

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Rpy-1.0.3 and R-2.13.1
by Assaf Gordon 22 Sep '11

22 Sep '11

Hello, It seems this issue (rpy) pops up every now and then: Has anyone managed to get rpy-1.0.3 working properly with R-13.1 (including loading packages) ? After compiling R-2.13.1 from source, and recompiling rpy-1.0.3, I get the following error when trying to load an R module through rpy: =================== $ python >>> import rpy >>> rpy.r.version["version.string"] 'R version 2.13.1 (2011-07-08)' ### Make sure the "limma" library is installed: >>> [ name for name in rpy.r.library()["results"] if name[0] == "limma" ] [['limma', '/usr/local/lib64/R/library', 'Linear Models for Microarray Data']] ### Trying to load 'limma' fails, with unspecified error: >>> rpy.r.library("limma") Traceback (most recent call last): File "<stdin>", line 1, in <module> rpy.RPy_RException: Error: package/namespace load failed for 'limma' ====================== I've checked that: 1. The "limma" library is definitely installed and loads properly from R. 2. Some libraries can be loaded from RPY (e.g. "stats", "tcltk", and others) 3. Many bioconductor libraries can't be loaded from RPY (but all load properly from R). 4. All of the above used to work in R-2.11.1 Any ideas ? Thanks, -gordon

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Loading Histories etc
by SHAUN WEBB 22 Sep '11

22 Sep '11

Hi, I have built up a large collection of Galaxy data on my local account and I am now finding the following operations very slow: Showing saved histories Refreshing a history containing many data items Opening a library with ~200 files Is there anyway to speed up performance? I am using a mysql database. Would postgres help? I am yet to see a reliable way of converting between mysql and postgres so haven't done this yet. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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DB on a remote host
by Nikolai Vazov 22 Sep '11

22 Sep '11

Hi, everybody, and Nate :) You helped me to configure an SSL connection to a DB on a remote host. It worked fine, but I have to do it again, on a RHEL6 (the one before was RHEL 5). I am using psycopg2-2.0.13 and followed all the steps given by Nate, yet it throws an error here: I run : % PYTHONPATH=/home/galaxy/galaxy-dist/scripts/scramble/lib python -v setup.py egg_info --tag-build=_8.4.2_static bdist_egg and get : +++++++++++++++++++++ ... running egg_info writing psycopg2.egg-info/PKG-INFO writing top-level names to psycopg2.egg-info/top_level.txt writing dependency_links to psycopg2.egg-info/dependency_links.txt # /usr/lib/python2.6/site-packages/setuptools/command/build_py.pyc matches /usr/lib/python2.6/site-packages/setuptools/command/build_py.py import setuptools.command.build_py # precompiled from /usr/lib/python2.6/site-packages/setuptools/command/build_py.pyc # /usr/lib64/python2.6/distutils/command/build_py.pyc matches /usr/lib64/python2.6/distutils/command/build_py.py import distutils.command.build_py # precompiled from /usr/lib64/python2.6/distutils/command/build_py.pyc # /usr/lib64/python2.6/distutils/command/build.pyc matches /usr/lib64/python2.6/distutils/command/build.py import distutils.command.build # precompiled from /usr/lib64/python2.6/distutils/command/build.pyc # /usr/lib64/python2.6/encodings/string_escape.pyc matches /usr/lib64/python2.6/encodings/string_escape.py import encodings.string_escape # precompiled from /usr/lib64/python2.6/encodings/string_escape.pyc error: No such file or directory # clear __builtin__._ # clear sys.path +++++++++++++++++++++ Which is the missing file/dir ? Thank you Nikolay -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo

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Installation troubles with numpy dependency
by Sebastian Bauer 20 Sep '11

20 Sep '11

Hi, we want to setup a local installation of Galaxy. It seems that Galaxy doesn't like the fact that we already have a different version of numpy installed. When following the installation instructions, we get following error messages: > Traceback (most recent call last): > File "./scripts/fetch_eggs.py", line 30, in <module> > c.resolve() # Only fetch eggs required by the config > File "/home/galaxy/galaxy-new/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve > egg.resolve() > File "/home/galaxy/galaxy-new/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve > return self.version_conflict( e.args[0], e.args[1] ) > File "/home/galaxy/galaxy-new/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) > File "/usr/lib/python2.6/dist-packages/pkg_resources.py", line 552, in resolve > raise DistributionNotFound(req) > pkg_resources.DistributionNotFound: numpy==1.6.0 Note that we are using Debian and have already numpy 1.4.1 installed. How can we solve this problem without deinstalling numpy 1.4.1 (due to other dependencies)? Thanks in advance! Best, Sebastian

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