- galaxy-dev - lists.galaxyproject.org

cloud instance missing /opt/sge/default/common directory
by Joseph Hargitai 27 Sep '11

27 Sep '11

Hi, Upon restarting a saved cloud instance I am missing: -bash: /opt/sge/default/common/settings.sh: No such file or directory -bash: /opt/sge/default/common/settings.sh: No such file or directory all the other mounts are there and well preserved. Is this pulled from a special place i may have not saved? The instance now does not boot beyond this point. Have login and admin console access. joe

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Export Galaxy workflows to gUSE workflows
by Sandra Gesing 26 Sep '11

26 Sep '11

Dear all, we work in different projects with two portals - Galaxy for our local clusters and WS-PGRADE for grid projects (e.g., MoSGrid, SCI-BUS) with the respective grid security infrastructure based on X.509 certificates. I developed for Galaxy an export of workflows to gUSE workflows. WS-PGRADE is a workflow-enabled grid portal and an user interface of gUSE. Please find below and attached more information on gUSE and WS-PGRADE. I would like to suggest this extension for Galaxy so that users could easily collaborate on Galaxy workflows and gUSE workflows. I had a look at your Galaxy Tool Shed but I'm not sure whether this is the right place to submit the extension. As far as I have seen, there are tool extensions and not extensions of basic features. For the export, I changed two files: * workflow.py (I added the function download_to_wspgrade_file) * export.mako (I added <%def name="render_download_to_wspgrade_file(item)">) Furthermore, two files are added: * wspgrade_download.mako * wspgrade_download_content.mako (All four files are attached.) Thank you for your time and consideration in this matter, Sandra Gesing University of Tübingen Applied Bioinformatics Group Sand 14 72076 Tübingen Germany Phone: +49-7071-2970456 ------------------------------------------------------------------------------- WS-PGRADE (Web Services Parallel Grid Runtime and Developer Environment) as graphical user interface of gUSE (grid User Support Environment) is the second generation of the workflow-enabled grid portal P-GRADE. The collaborative, community-oriented application development environment of WS-PGRADE offers a graphical workflow editor and enables the users to create, change, invoke, and monitor workflows. The latter may contain jobs on local resources and distributed resources in grid and cloud infrastructures. Existing workflows, workflow graphs, workflow templates, and sophisticated workflow applications can be shared via a local repository. gUSE is a virtualization environment providing a large set of high-level Distributed Computing Infrastructures (DCI) services by which interoperation among classical service and desktop grids, clouds and clusters, unique web services, and user communities can be achieved in a scalable way. Internally, gUSE is implemented as set of Web services, which dynamically provide user services in DCI and/or Web services environments. WS-PGRADE uses the client APIs of gUSE services to turn user requests into sequences of gUSE specific Web service calls. WS-PGRADE hides the communication protocols and sequences behind JSR168/JSR286 compliant portlets and its GUI can be accessed via Web browsers. See details of WS-PGRADE and gUSE at: http://www.guse.hu/ P-GRADE or WS-PGRADE, respectively, are used by * National Grid portals (UK, Ireland, Croatia, Turkey, Spain, Belgium, Malaysia , Kazakhstan, Switzerland, Australia, ClGrid, etc.) * HP-SEE/SEE-GRID-SCI, BalticGrid * US Open Science Grid, TeraGrid * IDGF (International Desktop Grid Federation) * SHIWA Simulation Platform * Economy-Grid, Swiss BioGrid, Bio és * Biomed Virtual Organisations, MathGrid, etc. * the German MosGrid project * EU FP7 EDGI * UK ProSim project * CancerGrid project A new 3-year, large FP7 Gateway project (called as SCIence gateway Based User Support - SCI-BUS) will be started in October as the flagship EU Gateway project with the goal of establishing 27 science gateways and portals (based on WS-PGRADE/gUSE) for various user communities and NGIs in Europe. gUSE/WS-PGRADE is open source and downloadable from sourceforge: http://sourceforge.net/projects/guse/ For further information you can read: P. Kacsuk: P-GRADE portal family for Grid infrastructures, Concurrency and Computation: Practice and Experience journal, Volume: 23, Issue: 3, 2011, pp. 235-245

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picard error.
by michael burrell (TOC) 26 Sep '11

26 Sep '11

Good afternoon, When starting galaxy I find the following errors logged in the paster.log galaxy.tools DEBUG 2011-09-26 13:58:21,577 Loaded tool: PicardASMetrics 0.03 galaxy.tools.test DEBUG 2011-09-26 13:58:21,625 Error in add_param for maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools DEBUG 2011-09-26 13:58:21,703 Loaded tool: PicardInsertSize 0.3.0 galaxy.tools.test DEBUG 2011-09-26 13:58:21,737 Error in add_param for maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure that the parameter exists and that any container groups are defined first. Our galaxy version is. galaxy@jic55666:~/software/galaxy-central$ hg tip changeset: 6042:2469c53051ea tag: tip user: Daniel Blankenberg <dan(a)bx.psu.edu> date: Sun Sep 25 13:27:14 2011 -0400 summary: Some random lines tool tweaks. Thank you for your assistance. Michael. ----------------------------------------------------------------------------------------------------- Please note, that my email address is no longer givenname.surname(a)bbsrc.ac.uk. Please update your records to reflect my new email address of givenname.surname(a)nbi.ac.uk as shown on this email.

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Error in FastQC
by Matthew J. Thomas 26 Sep '11

26 Sep '11

Hello, I am working on a local install of Galaxy and when running a test data set I get this error when invoking the Fastqc commans: /home/mnkyboy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 20 class FastQC(): ^ SyntaxError: invalid syntax This is Illumina data from a single tile of qseq.txt data converted to FASTQ and run through the FASTQ groomer. Fastqc is working properly outside of Galaxy so any advice would be appreciated. Thanks, Matt T.

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Re: [galaxy-dev] Specifying a range of inputs?
by Peter Cock 24 Sep '11

24 Sep '11

I realise we went off list accidentally. On Saturday, September 24, 2011, Timothy Wu <2huggie(a)gmail.com> wrote: > On Sat, Sep 24, 2011 at 6:52 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: >> >> Elegant maybe, but the UI side does not seem >> practical with the current Galaxy. > > Is there any future plan for a better multiple file support? It has been discussed a little in other contexts, Like running a workflow many times in parallel. >> >> I would write a tool to get the data from the NCBI into >> Galaxy as a single FASTA file in this situation. I'm >> assuming there is some rule to pick the particular >> set (e.g. An Entrez search, perhaps by taxonomy). > > Yeah, I think that's what I'll have to do. Thanks. :) > > Timothy Peter

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Re: [galaxy-dev] use_tasked_jobs
by Chorny, Ilya 24 Sep '11

24 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 24 Sep '11

24 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 24 Sep '11

24 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 24 Sep '11

24 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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