- galaxy-dev - lists.galaxyproject.org

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 23 Sep '11

23 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 23 Sep '11

23 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 23 Sep '11

23 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 21 Sep '11

21 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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Re: [galaxy-dev] Galaxy Tool permission/Access
by Hotz, Hans-Rudolf 20 Sep '11

20 Sep '11

On 09/19/2011 04:35 PM, sohkhan(a)notes.cc.sunysb.edu wrote: > Hi, > > I am wondering if there is way to manage user access to Galaxy tools? > > I.E, certain users are restricted to use certain tools. > Thanks. Hi Sohail We use a 'quick and dirty' solution by enforcing log-in and then taking advantage of the reserved variables "$__user_email__" (see: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) add "$__user_email__" to the command line, eg: <command interpreter="perl"> access_data.pl $dir $userEmail $output </command> and then use a little wrapper, or do the test in the script itself, eg: my $priv_user = "geek\(a)fmi.ch"; my $file = $ARGV[0]; my $user = $ARGV[1]; unless ($user eq $priv_user) { print "you don't have access to this data"; exit; } open (FILE, "$file"); ... of coursde, instead of hard coding, you can expand this by using a little database where you store all the 'privileged users'. Regards, Hans > > -Sohail > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/

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Writing Galaxy Extensions involving Workflows
by Oren Livne 20 Sep '11

20 Sep '11

Dear All, I am a software developer, new to Galaxy. Is there a detailed document about the Galaxy code architecture, API, what runners are, and how to write a runner that has access to the workflow object model? I could not find this information on the Galaxy Wiki. I am especially interested in integrating Galaxy with an external scheduler software (I am aware of Galaxy's scheduling capabilities but we'd like to use our own). My goal is to intercept Galaxy workflow run events and send workflows to my scheduler.I could not find this information on the Galaxy Wiki. Thank you so much in advance, Oren Livne

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Error Using Intersect Tool on Genomic Intervals
by Chamith Fonseka 20 Sep '11

20 Sep '11

Hello, I am trying to use Galaxy to intersect different sets of genomic intervals. When I do this, I get the following error. Skipped 10 invalid lines of 1st dataset, 1st line #20: "chr10 131694149 131694408", problem: 536870912 is larger than the size of this BitSet (536870912). I have tried using different sets of intervals, in both interval and BED format and used the two queries in different order in the intersect tool, but I cannot seem to resolve the problem. The error message will differ in the number of "invalid lines" skipped, but when I check the intervals they appear to be alright. Could anyone help? Thank you very much, Chamith Fonseka

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Query related to BLAST
by Jennifer Jackson 20 Sep '11

20 Sep '11

Hi Kumar, I am going to forward this question to the Galaxy Development discussion list for others to offer input, but here are the basics: Wiki: http://galaxyproject.org/wiki/Admin/Tools/External%20Display%20Applications… Archived mailing list responses on this topic: http://gmod.827538.n3.nabble.com/galaxy-dev-adding-another-UCSC-mirror-to-d… http://gmod.827538.n3.nabble.com/UCSC-genome-browser-tt1911708.html#a2039796 http://gmod.827538.n3.nabble.com/Re-Genome-UCSC-browser-access-from-Galaxy-… Other configuration help: http://galaxyproject.org/wiki/Admin http://galaxyproject.org/wiki/Admin/Config/Apache%20Proxy http://galaxyproject.org/wiki/Admin/Data%20Integration http://galaxyproject.org/wiki/Config/Performance/Production%20Server Hopefully this helps! Best, Jen Galaxy team On 9/19/11 4:24 AM, kumar Saurabh wrote: > Dear Jen, > > Thank you for the reply. I have one more query. > > Currently, Galaxy tool is integrated with the UCSC genome browser and > that is the way it operates. You can retrieve any region from the human > and other available genome (Available with UCSC) and analyze the data or > create the workflows. We can even upload the data in various file formats. > > I was wondering if there is any option available or is it possible to > integrate the Galaxy tool with our own customised genome browser/genome > databases? I just would like to confirm if its possible to integrate the > local version of galaxy with our own genome browsers. If yes, can we > also connect it to multiple genome browsers? > > Best regards, > Kumar > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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MACS.html download error
by Susan Newman 20 Sep '11

20 Sep '11

Hi, I am running the public instance of Galaxy. I've successfully run multiple histories using MACS. Recently, I am unable to download the MACS.html file. The MACS steps have run successfully and they are green. When I click on the diskette icon to download I get this message "Unable to remove temporary download and archive file directory". In addition, I am sharing the history with another user. He sees a server error when he clicks any of the file links to the .xls files when he uses the eye icon to view the MACS.html data within Galaxy. I am able to use the links within my own Galaxy account. Thanks for your assistance, Susan Susan S. Newman, Laboratory Manager Genomics Core Facility, L2012 Pennington Biomedical Research Center 6400 Perkins Road Baton Rouge, LA 70808 225-763-0255 (o) 225-763-0257 (lab) http://gcf.pbrc.edu

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