- galaxy-dev - lists.galaxyproject.org

barchart not working: GNUplot problem
by Joachim Jacob 12 Sep '11

12 Sep '11

Hi all, I have got numpy and gnuplot on speaking terms. But now, trying to use the barchart, I get following error: gnuplot> set style histogram clustered gap 5 title offset character 0, 0, 0 ^ line 0: expecting 'data', 'function', 'line', 'fill' or 'arrow' line 0: undefined variable: in line 0: undefined variable: invert gnuplot> set style data histograms ^ line 0: expecting 'lines', 'points', 'linespoints', 'dots', 'impulses', 'yerrorbars', 'xerrorbars', 'xyerrorbars', 'steps', 'fsteps', 'histeps', 'filledcurves', 'boxes', 'boxerrorbars', 'boxxyerrorbars', 'vectors', 'financebars', 'candlesticks', 'errorlines', 'xerrorlines', 'yerrorlines', 'xyerrorlines', 'pm3d' Gnuplot is working from commandline and has version 4.0. Thanks for any suggestion! Joachim

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Installing tools with dependencies using mi-deployment scripts
by Mattias de Hollander 12 Sep '11

12 Sep '11

Hello, I am trying to add tools (PyCogent, Qiime) to a Cloudman image using the mi-deployment scripts. Qiime depends on PyCogent and it needs to be accessible on the python path, otherwise I get an error: PyCogent not installed but required. (Is it installed? Is it in the current user's $PYTHONPATH or site-packages?) Is there a way to add the paths in env.sh to the sys.path during installation using tools_fabfile.py? All the tools are in /mnt/galaxyTools/tools. I tried the DependencyManager from galaxy but then I only receive the path to the env.sh file: In [43]: dependency_manager.find_dep('blast') Out[43]: ('/mnt/galaxyTools/tools/blast/2.2.25/env.sh', '/mnt/galaxyTools/tools/blast/2.2.25', '2.2.25') Is there a smarter way to add files to the PYTHONPATH during the execution of tools_fabfile.py? Thanks, Mattias -- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands

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bam grooming
by Paul Igor Costea 12 Sep '11

12 Sep '11

Hello, I am new at using the galaxy server and i have come across an annoying restriction when it comes to bam files. There is an assumption build in, that a bam file needs to be coordinate sorted. (does hold for most tools). However, most of my tools are using the bam file coming off the mapper. (saves some time by not having to do sorting). Is there any way to get around this restriction? Right now i've hacked it to always return false for binary.py::dataset_content_needs_grooming. I do however think that this could be a property of the bam file. A classification of the sort "Unkown", "Name Sorted", "Position sorted" sounds like a good idea to me. Regards, -Paul

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Command line option
by Timothy Wu 10 Sep '11

10 Sep '11

Hi, I'm putting my own tool into Galaxy. Suppose I have an command line option that is designated by a switch. Such as $executable.py -a option input output The "-a option" is an optional argument. I want to make sure when the option is not given, "-a option" is entirely taken out. I tried Cheetah script like this (this fails): <command interpreter="python">executable #if $option != None -a $option #end if $input $output</command> This $option is suppose to be an optional tabular file and is written within <param> as: <param name="option" type="data" format="tabular" label="XXX" optional="true"/> Somehow "-a None" is always printed (as seen from the server print-to-screen). But I thought I checked explicitly for it to be anything but None. Then I realized that type($option) <class 'galaxy.tools.DatasetFilenameWrapper'>. So I coerced both that and NoneType into string prior to checking for equality. Is this the proper way to do it? Timothy

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Exporting Galaxy Pages to another Galaxy server
by Kempenaar, M (med) 10 Sep '11

10 Sep '11

Hi, I was wondering if it is possible to export a Galaxy Page to another Galaxy server. Currently I'm using a development server and a production server and I have a Galaxy Page containing a manual with example data etc. that I'd like to make available on the production server. Also, since I sometimes distribute a virtual machine running galaxy to users (with instructions / scripts to keep software etc. up-to-date) and like to be able to share a page with them on their own server. I expect a Page to be in the database instead of a simple file on disk, so probably it requires database work. Thanks for any help! ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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default quotas by mail domain
by Edward Kirton 09 Sep '11

09 Sep '11

with the new quotas, there's nothing to prevent a user from generating multiple accounts using assorted free email accounts. may i suggest the ability to have default quotas by mail domain? i would like to give gmail/yahoo or *.com users tiny quotas, larger quotas for *.edu, *.gov users, and largest quotas for users with our own mail domains e.g. @lbl.gov. alternatively i'd like to limit user registration by mail domain (disallow gmail, etc.). comments?

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Server Error
by Alex R Bigelow 09 Sep '11

09 Sep '11

Hi, I am a new developer interested in writing tools for Galaxy, but when I try to use the tool shed (http://toolshed.g2.bx.psu.edu) every link I click on gives me a Server Error. I have tried in both Google Chrome and Safari; does anyone know what is going on? Thanks, Alex Bigelow

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cuffcompare wrapper
by Chorny, Ilya 08 Sep '11

08 Sep '11

Hi Jeremy, The symlink in the cuffcompare wrapper was causing galaxy to crash because I run as the actual user and have to chmod the job_working directory at the end so Galaxy can clean it up. Turns out is seems like the symlink is not needed. Am I missing something. See below. Your code: for i, arg in enumerate( args ): input_file_name = "./input%i" % ( i+1 ) os.symlink( arg, input_file_name ) cmd += "%s " % input_file_name My code: for i, arg in enumerate( args ): cmd += arg 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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Re: [galaxy-dev] galaxy-dev Digest, Vol 63, Issue 8
by Andrew Warren 08 Sep '11

08 Sep '11

I would also like to voice my support for this feature. I wrote a wrapper for bowtie that converts the SAM output to BAM after bowtie is finished just to avoid the hassle of letting galaxy "know" that the SAM file existed (didn't want to run Tophat). After thinking about how I would go about deleting an existing output it occurred to me that a "deleting tool" would require some extra logic since you would probably want to prevent the output port on a workflow node/tool from being connected to the input of another node if the output is going to be deleted. I was wondering if it might make sense to modify the "flagged output" feature (the asterisk) of the galaxy tools nodes to delete the non-flagged outputs instead of just hiding them? Or perhaps just mark them as deleted so they will be taken care of by the cleanup scripts? In this same line of thinking, it might make sense to have a flag for the input ports that specify that the input will be consumed/deleted after the tool has successfully run. This would address the case where you wanted to use the output of a tool before it is removed. Cheers, Andrew >I haven't had a chance to do anything on this yet, but I'll see if I can work something out in the near future.> > >-Dannon > >On Sep 7, 2011, at 9:34 PM, Glen Beane wrote: > > > On Sep 7, 2011, at 8:10 PM, Edward Kirton wrote: > >> i'm resurrecting this thread to see if there's any more support for the idea of deleting intermediate files in a workflow. i think this is an important feature to have. oftentimes a workflow creates many intermediate files no one will ever look at. and leaving it up to the user to cleanup their data files is asking too much. there's another ticket regarding allow users to still be able to preview the metadata of deleted workflow history items and together these would go together nicely. >> > > I am _very_ interested in this feature > > -- > Glen L. Beane > Senior Software Engineer > The Jackson Laboratory > (207) 288-6153 > > > ___________________________________________________________ > 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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Installation error
by IT Support 08 Sep '11

08 Sep '11

Greetings, I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to a location commonly accessible by all analysis nodes. I then set the path to Python 2.7 like so: export PATH=/opt/galaxy-python/python:$PATH However, executing run.sh gives me the error at the end of this message. The strange thing is that Galaxy runs fine on a CentOS 5.6 virtual machine. Any help would be much appreciated. Thanks! ----- Traceback (most recent call last): File "./scripts/paster.py", line 34, in ? command.run() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 218, in run result = self.command() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 311, in loadapp return loadapp( File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/opt/galaxy-dist/lib/galaxy/web/controllers/admin.py", line 310 link=( lambda item: (dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) if not item.default else dict( operation="Change amount", id=item.id, webapp="galaxy" )) ), -----

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