May 2013 - galaxy-dev - lists.galaxyproject.org

Recall: [External] Re: [galaxy-user] Question on galaxy data visualization
by Sun, Wenping [USA] 16 May '13

16 May '13

Sun, Wenping [USA] would like to recall the message, "[External] Re: [galaxy-user] Question on galaxy data visualization".

1 0

Re: [galaxy-dev] [External] Re: [galaxy-user] Question on galaxy data visualization
by Sun, Wenping [USA] 16 May '13

16 May '13

Jen, Thank you for the information. I am using galaxy cloud to try the trickster for one of the processed chipseq analysis. However, there is no visualization for the bed file created from galaxy. Meantime, I am having problem to get back to galaxy now. Here is the error message as below -- The proxy could not connect to the destination in time. URL: http://ec2-107-20-10-72.compute-1.amazonaws.com/cloud I have tried to re-launch the cloud instance, as well as directly access the DNS from aws, and keep getting the same error. Is this the bug? Please help to fix this since I have data there. Thanks! Kathryn From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Monday, May 13, 2013 6:18 PM To: Sun, Wenping [USA] Cc: galaxy-user(a)lists.bx.psu.edu Subject: [External] Re: [galaxy-user] Question on galaxy data visualization Hello Kathryn, Trackster is the primary data visualization tool and can be accessed by clicking on the mini graph icon within a dataset: [cid:image001.png@01CE5244.3D2016D0] or by going to "Visualization" in the upper menu bar and starting a new track browser. http://wiki.galaxyproject.org/Learn#Visualization If you are interested, for certain datasets, the icon will also offer other options: Circster and/or Scatterplot. The tool group "Graph/Display Data" has graphing tools and tools that prepare data to be visualized. The tool group "Motif Tools" has a sequence logo generator, and the groups " NGS: QC and manipulation" and " BEDTools" have more graphing tools. Hopefully this helps, Jen Galaxy team On 5/13/13 11:08 AM, Sun, Wenping [USA] wrote: Dear galaxy group, I have question on the data visualization from output of galaxy pipeline. Is there any ideogram tool inside of galaxy? Regards, Kathryn ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

1 0

Can't delete empty folder via Tool Shed web interface
by Peter Cock 16 May '13

16 May '13

Hi all, Due to some hickups with tar balls, I've been left with an unwanted empty folder: http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803 Trying to delete the folder has no effect - "No changes to repository " - is this a minor bug, or deliberate? [image: Inline image 1] Thanks, Peter

2 2

memdump
by Nikos Sidiropoulos 16 May '13

16 May '13

Hi everybody Has anybody used the "profile memory usage" feature, and if so, what are the benefits and the compromises of it? I'm trying to find documentation about it, without any luck. Thanks Nikos

2 1

Testing with <repeat> parameters
by Peter Cock 16 May '13

16 May '13

Hello all, Should unit tests with repeat parameters work? If so, how do I give each repeat group in the XML for the <test>? Sample tool here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list <inputs> <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/> <conditional name="universe"> <param name="type_select" type="select" label="Implicit or explicit full ID list?"> <option value="explicit">Explicit</option> <option value="implicit">Implicit (use union of sets below)</option> </param> <when value="explicit"> <param name="main" type="data" format="tabular,fasta,fastq,sff" label="Full dataset (with all identifiers)" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/> </when> <when value="implicit"/> </conditional> <repeat name="sets" min="1" max="3" title="Sets"> <param name="set" type="data" format="tabular,fasta,fastq,sff" label="Members of set" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/> <param name="lab" size="30" type="text" value="Group" label="Caption for set"/> </repeat> </inputs> The first test attempts to use the repeat "set"/"lab" once - guessing at how to give repeat parameters in a test: <test> <param name="type_select" value="explicit"/> <param name="main" value="venn_list.tabular" ftype="tabular"/> <param name="main_lab" value="Some Proteins"/> <param name="set" value="rhodopsin_proteins.fasta"/> <param name="lab" value="Rhodopsins"/> <output name="PDF" file="venn_list1.pdf" ftype="pdf"/> </test> $ ./run_functional_tests.sh -id venn_list ... python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular "Some Proteins" /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta "Rhodopsins" /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta "Group" /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat ... This seems to have resulted in two <repeat> entries, and so fails. What I was expecting was: python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular "Some Proteins" /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta "Rhodopsins" /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat Thanks, Peter

1 0

rpy2 Core Tools
by John Chilton 16 May '13

16 May '13

I had promised these to someone on a bitbucket issue years ago and I said I would send them to Dannon and Nate on IRC today, so I am just going to spam these out far and wide. These are the MSI versions of many of the core tools that have been rewritten to target rpy2 instead of rpy . Caveat emptor, these were never meant for external consumption. It looks like the ones we never got to include: rgenetics/rgQC.py, regVariation/rcve.py, ngs_simulation/ngs_simulation.py, metag_tools/short_reads_figure_high_quality_length.py, and taxonomy/poisson2test.py. -John

2 1

History page not opening
by sridhar srinivasan 16 May '13

16 May '13

Hi after installing galaxy, i could'nt see the history page in right end of galaxy web. it shows """ Content Encoding Error The page you are trying to view cannot be shown because it uses an invalid or unsupported form of compression. * Please contact the website owners to inform them of this problem. """ Please help me to solve the issue.. sridhar

2 3

selecting multiple inputs for workflows not possible
by Joachim Jacob | VIB | 16 May '13

16 May '13

Hi all, I just found out that I cannot select multiple inputs in workflows. This option used to work on these workflows in the past. I am a little puzzled of what's wrong. Any light in the dark? Note: I have started a cloud galaxy instance and imported that workflow, but no option to select multiple inputs. Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

2 1

memdump
by Nikos Sidiropoulos 16 May '13

16 May '13

Hi everybody Has anybody used the "profile memory usage" feature, and if so, what are the benefits and the compromises of it? I'm trying to find documentation about it, without any luck. Thanks Nikos

1 0

Re: [galaxy-dev] starting run_reports.sh fails
by Joachim Jacob | VIB | 16 May '13

16 May '13

No prob. Actually, I have found the answer thanks to the GalaxyAdmins meeting yesterday, where somebody extensively pointed to Trello ;-) Cheers J Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 05/15/2013 07:00 PM, Dannon Baker wrote: > Heh, thanks for answering both halves of the email before I could even > get to it :) > > > On Wed, May 15, 2013 at 12:03 PM, Joachim Jacob | VIB | > <joachim.jacob(a)vib.be <mailto:joachim.jacob@vib.be>> wrote: > > Already reported in Trello > https://trello.com/c/o0S3klAF > > Thanks for the fix! > > > Joachim Jacob > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 <tel:%2B32%209%20244.66.34> > Bioinformatics Training and Services (BITS) > http://www.bits.vib.be > @bitsatvib > > On 05/15/2013 03:19 PM, Joachim Jacob | VIB | wrote: > > run_reports.sh dies silently. > > Its last will in reports_webapp.log states: > > Traceback (most recent call last): > File "./scripts/paster.py", line 33, in <module> > serve.run() > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", > line 1056, in run > invoke(command, command_name, options, args[1:]) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", > line 1062, in invoke > exit_code = runner.run(args) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", > line 227, in run > result = self.command() > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", > line 650, in command > app = loadapp( app_spec, name=app_name, relative_to=base, > global_conf=vars) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 350, in loadapp > return loadobj(APP, uri, name=name, **kw) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 375, in loadobj > return context.create() > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 813, in create > return self.object_type.invoke(self) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 249, in invoke > return fix_call(context.object, context.global_conf, > **context.local_conf) > File > "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", > line 97, in fix_call > val = callable(*args, **kw) > File > "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py", > line 61, in app_factory > add_ui_controllers( webapp, app ) > File > "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py", > line 33, in add_ui_controllers > from galaxy.web.base.controller import BaseUIController > File > "/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py", > line 23, in <module> > from galaxy.visualization.genome.visual_analytics import > get_tool_def > File > "/home/galaxy/galaxy-dist/lib/galaxy/visualization/genome/visual_analytics.py", > line 3, in <module> > from galaxy.tools.parameters.basic import > IntegerToolParameter, FloatToolParameter, SelectToolParameter > File > "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line > 57, in <module> > from galaxy.visualization.genome.visual_analytics import > TracksterConfig > ImportError: cannot import name TracksterConfig > > Anybody knowing the recipe to reanimate the patient? Thanks. > BTW, this is the first time I am starting up run_reports.sh > after the 1 april/8 april update. Did not had this issue before. > > > Joachim > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > >

1 0