- galaxy-dev - lists.galaxyproject.org

Published Workflows menu location
by Peter Cock 18 May '11

18 May '11

Hi all, I recently started trying out the "Share workflow" functionality on our local Galaxy, so that I could make available some general interest workflows to all our users, rather than sharing them with individuals one by one. However, once published, it was not easy to find them! I eventually found them under the "Shared Data" drop down menu entry "Published Workflows" (yet "Shared" workflows are not on this menu). The captions "Shared" and "Published" seem to be used inconsistently. Maybe the top level "Shared Data" menu should be renamed to "Shared Resources" or "Published Resources"? To me, workflows are not data, and so should not be under "Shared Data". Rather, I expected them to be under the "Workflow" menu. Is the separation because in order to run or edit a "Published Workflows", you must first import it? Perhaps a simple solution would be a note and link at the bottom of the main "Workflow" page directing people to the "Published Workflows" page under the "Shared Data" drop down menu. Peter

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Select first/last N rows from grouped tabular files (e.g. top BLAST hits)
by Peter Cock 18 May '11

18 May '11

Hi all, I'm wondering if the following task can be done in Galaxy with the standard tools. The specific example is selecting the top (e.g. 3) match sequences for each blast query, but I see this problem as much more general than a "Select top BLAST hits" tool. I want to select the first few (e.g. 1) rows of each group in a tabular file, where the group criteria is having certain columns equal (e.g. the first 2). e.g. Tabular BLAST output has columns of query ID, match ID, etc. queryA match1 ... queryA match2 ... queryA match2 ... queryA match3 ... queryA match4 ... queryA match4 ... queryA match4 ... queryB match5 ... queryB match5 ... queryC match6 ... queryC match7 ... In this example, some of my queries have more than one HSP per match (more than one line with the same first two columns). If I group on the first two columns, the groups are: ------------------------ queryA match1 ... ------------------------ queryA match2 ... queryA match2 ... ------------------------ queryA match3 ... ------------------------ queryA match4 ... queryA match4 ... queryA match4 ... ------------------------ queryB match5 ... queryB match5 ... ------------------------ queryC match6 ... ------------------------ queryC match7 ... ------------------------ If I then take the first row in each group, that gives me just the first HSP for each query+match combination. queryA match1 ... queryA match2 ... queryA match3 ... queryA match4 ... queryB match5 ... queryC match6 ... queryC match7 ... If for example I wanted only the top 3 matches for each query, I could repeat the proposed tool one more time but with different settings - this time grouping on the first column only: queryA match1 ... queryA match2 ... queryA match3 ... queryB match5 ... queryC match6 ... queryC match7 ... I hope I've conveyed the idea here. The existing tools "Select first lines from a dataset" and "Select last lines from a dataset" are related, but do this at the file level. Does this make sense? Does it seem like a useful tool to write if there isn't anything like this already present? Or might it be simpler to just write a "Select top BLAST hits" tool? Peter

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Reciprocal Best Hits (RBH) from BLAST tabular output
by Peter Cock 18 May '11

18 May '11

Hi all, I mentioned just over a month ago that I had written a Galaxy tool to do find Reciprocal Best Hits (RBH) from BLAST tabular output or similar (e.g. Bill Pearson's FASTA tabular output). http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004825.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004829.html The only problem I had was setting default columns, which I consider to be a minor bug in Galaxy: https://bitbucket.org/galaxy/galaxy-central/issue/507 Regardless of this small usability issue, would the Galaxy team like to add this tool to the main distribution (to sit along with my BLAST+ wrappers), or should I submit it to the tool shed? If you want to merge it, the following change set should suffice: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 I made a subsequent change set to test giving column defaults as value="c2" rather than value="c2" which makes no difference, but if this is how default column values are meant to be given, take this change too: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 Thanks, Peter

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galaxy doesn't start with drmaa job runner
by Shantanu Pavgi 17 May '11

17 May '11

I am trying to configure galaxy with sge/drmaa scheduler. The galaxy process is starting up fine without any drmaa configuration. However the galaxy daemon doesn't start properly when I add drmaa configuration lines as shown below. I have set SGE_ROOT and DRMAA_LIBRARY_PATH variables properly. Am I missing something important here? # drmaa configuration: {{{ start_job_runners = drmaa default_cluster_job_runner = drmaa:/// }} # paster.log file - with drmaa config the process dies with "Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner" as last line in the log file. With local job runner the galaxy starts fine as shown below: {{{ galaxy.jobs DEBUG 2011-05-17 09:59:58,959 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs INFO 2011-05-17 09:59:58,959 job manager started galaxy.jobs INFO 2011-05-17 09:59:59,325 job stopper started galaxy.sample_tracking.external_service_types DEBUG 2011-05-17 09:59:59,330 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2011-05-17 09:59:59,333 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,349 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,417 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,435 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,451 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,455 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,474 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,480 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,549 Enabling 'tracks' controller, class: TracksController galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,550 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,556 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,561 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,562 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,746 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,752 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,756 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,026 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,031 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,090 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,095 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,104 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,137 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,143 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,148 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,158 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,165 Enabling 'root' controller, class: RootController galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,189 Enabling 'httpexceptions' middleware galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,195 Enabling 'recursive' middleware galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,220 Enabling 'print debug' middleware /share/apps/galaxy/shantanu-temp-workspace/galaxy-cluster-test/galaxy-dist-50e249442c5a/eggs/WebError-0.8a-py2.6.egg/weberror/exceptions/serial_number_generator.py:11: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,726 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,740 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,740 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,744 Enabling 'x-forwarded-host' middleware Starting server in PID 10170. serving on 0.0.0.0:8081 view at http://127.0.0.1:8081 }}} -- Thanks, Shantanu.

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Re: [galaxy-dev] [Galaxy #14246] Select first/last N rows from grouped tabular files (e.g. top BLAST hits)
by Peter Cock 17 May '11

17 May '11

On Tue, May 17, 2011 at 5:30 PM, Galaxy Support Tickets <galaxy(a)ci.uchicago.edu> wrote: > Dear Galaxy@iBi user: > > This message has been automatically generated in response to the creation of > a Galaxy@iBi request regarding: > > "Select first/last N rows from grouped tabular files (e.g. top BLAST hits)" > > Your ticket has been assigned an ID of [Galaxy #14246]. > > > Please include the string: > > [Galaxy #14246] > This continues a discussion started under your reference [Galaxy #13918], assigned to Alex Rodriguez. Peter

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Database/Build
by Dave Walton 17 May '11

17 May '11

I'd like to get a better understanding of the point of the database/build attribute, and pose the question of when is the appropriate time to have it set? In our case at the Jackson Laboratory, the most common build is NCBI37/MM9. However, the feeling of many folks here, is that this should not be set on our fastq files. The only place we really run into trouble is with cufflinks. If you haven't set the db when you get to cufflinks you'll get an error. Our suggestion is that there should be one of two options: 1) Tophat has the ability to set the database of the output files based on the genome that was selected for alignment. 2) There should be a module that can be plugged into a workflow that would set the database of the file prior to passing the file to cufflinks (or any other two that requires the database attribute to be set). We are curious if anyone else is running into this issue, and how it is being solved. We're thinking about hacking the Tophat wrapper, but I wanted to check with others before I did this. Thanks, Dave

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Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from vadimverenich@gmail.com
by Ross 17 May '11

17 May '11

Hi, thanks for reporting this error. Ploteig is a perl script that is part of the eigensoft package and it seems to be inaccessible while eigensoft is executing judging from the error message. We'll fix this as soon as we can. Meanwhile, in case you didn't check, I noticed that if you click on the eye icon of items 2 and 4 in your history, the eigenplot is there - even though the history items are in an error state...I'm not sure I understand exactly how this has happened but it did. The way the samples are labelled (all are 'sample') on the plot is not very informative - I need to look more closely at the data to see how we can make the plot more useful. On Mon, May 16, 2011 at 9:48 PM, <galaxy-bugs(a)bx.psu.edu> wrote: > > GALAXY TOOL ERROR REPORT > ------------------------ > > This error report was sent from the Galaxy instance hosted on the server > "main.g2.bx.psu.edu" > ----------------------------------------------------------------------------- > This is in reference to dataset id 2452824 from history id 554342 > ----------------------------------------------------------------------------- > You should be able to view the history containing the related history item > > 3: Ancestry PCA_rgEig.txt > > by logging in as a Galaxy admin user to the Galaxy instance referenced above > and pointing your browser to the following link. > > main.g2.bx.psu.edu/history/view?id=1f6151421eac94f6 > ----------------------------------------------------------------------------- > The user 'vadimverenich(a)gmail.com' provided the following information: > > sh: ploteig: not found > > ----------------------------------------------------------------------------- > job id: 2167094 > tool id: rgEigPCA1 > ----------------------------------------------------------------------------- > job command line: > python /galaxy/home/g2main/galaxy_main/tools/rgenetics/rgEigPCA.py "/galaxy/main_database/files/002/452/dataset_2452822_files/MDLD" "Ancestry PCA" "/galaxy/main_pool/pool5/tmp/job_working_directory/2167094/galaxy_dataset_2452823.dat" "/galaxy/main_pool/pool5/tmp/job_working_directory/2167094/dataset_2452823_files" "4" "5" "5" "6" "/galaxy/main_pool/pool5/tmp/job_working_directory/2167094/galaxy_dataset_2452824.dat" > ----------------------------------------------------------------------------- > job stderr: > sh: ploteig: not found > > ----------------------------------------------------------------------------- > job stdout: > smartpca -p Ancestry_PCA_pca.xls.par >Ancestry_PCA_log.txt > ploteig -i Ancestry_PCA_pca.xls.evec -c 1:2 -p ??? -x -y -o Ancestry_PCA_eigensoftplot.pdf.xtxt > evec2pca.perl 4 Ancestry_PCA_pca.xls.evec /galaxy/main_database/files/002/452/dataset_2452822_files/MDLD.fam Ancestry_PCA_pca.xls > rgEigPCA.py got /galaxy/home/g2main/galaxy_main/tools/rgenetics/rgEigPCA.py /galaxy/main_database/files/002/452/dataset_2452822_files/MDLD Ancestry PCA /galaxy/main_pool/pool5/tmp/job_working_directory/2167094/galaxy_dataset_2452823.dat /galaxy/main_pool/pool5/tmp/job_working_directory/2167094/dataset_2452823_files 4 5 5 6 /galaxy/main_pool/pool5/tmp/job_working_directory/2167094/galaxy_dataset_2452824.dat > llist=c("???") > glist=c(2) > par(lab=c(10,10,10)) > par(mai=c(1,1,1,0.5)) > pdf("Ancestry_PCA_PCAPlot.pdf",h=8,w=10) > par(lab=c(10,10,10)) > pca1 = c(0.076000,0.083300,0.072000,0.077100,0.079000,0.070600,0.082900,0.077600,0.077900,0.075400,0.076500,0.071000,0.070000,0.070600,0.072800,0.073100,0.068000,0.066700,0.073700,0.073400,0.074000,0.078700,0.077000,0.080100,0.063700,0.081400,0.077000,0.082500,0.083500,0.064900,0.072500,0.075200,0.078200,0.064600,0.051800,0.076600,0.059900,0.062800,0.058200,0.052800,0.060600,0.064300,0.049700,0.054000,0.058300,0.051700,0.057700,0.042700,0.046800,0.038700,0.048200,0.058600,0.035800,0.039700,0.043700,0.041300,0.033800,0.038400,0.042000,0.030600,0.042200,0.046200,0.039500,0.036500,0.039400,0.045200,0.085400,0.085600,0.084800,0.098500,0.093700,0.071400,0.088400,0.090300,0.096300,0.096900,-0.109500,-0.107400,-0.098500,-0.102900,-0.108700,-0.102900,-0.102000,-0.103400,-0.104600,-0.105300,-0.105100,-0.072000,-0.111300,-0.070000,-0.112000,-0.100200,-0.114700,-0.103900,-0.005000,-0.068300,0.018600,0.002600,0.012400,-0.000600,0.014100,0.012000,0.018300,0.011800,0.003600,0.022300,0.008! > 900,0.012900,0.023900,0.084100,0.077700,0.075600,0.070000,0.077800,0.064400,0.082800,0.067100,0.064200,0.075200,0.064400,0.057500,0.056000,0.052400,0.058800,0.052600,-0.061100,-0.014800,0.047700,-0.056900,0.053200,-0.070900,0.060200,-0.070600,-0.075800,0.059800,-0.049500,0.056200,-0.073500,-0.037000,-0.055400,-0.074600,-0.068600,0.067800,0.055900,-0.072600,-0.069500,-0.077800,-0.068600,-0.070900,0.043300,0.070400,0.068000,-0.014200,-0.024000,-0.020600,-0.020400,-0.012500,-0.010300,-0.020700,-0.025500,-0.034300,-0.018900,-0.018200,-0.017100,-0.012900,-0.032600,-0.040300,-0.058900,-0.061900,-0.067100,-0.062300,-0.062800,-0.070300,-0.063700,-0.065000,-0.078900,-0.068800,-0.053300,-0.050400,-0.067800,-0.055600,-0.065300,-0.052000,-0.054400,-0.065400,-0.069000,-0.080300,-0.089400,-0.087900,-0.090100,-0.007800,-0.084000,-0.087500,-0.095700,-0.087700,-0.099300,-0.062100,-0.006700,-0.084200,-0.086400,-0.087500,-0.101600,0.033600,-0.096300,-0.090500,-0.044900,-0.055000,-0.049300,-0.! > 054800,-0.059400,-0.061200,-0.055100,-0.052100,-0.055900,-0.050800,-0. > 063800,-0.055800,-0.061500,-0.057900,-0.065100,-0.056400,-0.057900,-0.044500) > pca2 = c(0.007500,0.001300,0.012400,0.000100,-0.001100,0.004400,0.013100,0.015700,0.015300,0.016800,0.000100,0.008200,0.008700,0.006900,0.004600,0.018400,0.003400,0.007400,0.004600,0.023700,-0.001200,-0.008500,0.015300,0.003300,-0.034300,-0.030100,-0.052700,-0.040700,-0.035400,-0.027100,-0.030700,-0.037700,-0.035500,0.117400,0.112900,-0.012000,0.118600,0.126200,0.118500,0.115200,0.118300,0.087600,0.105900,0.111500,0.118000,0.090500,0.111500,-0.026600,-0.034800,-0.047100,-0.036100,-0.040500,-0.042900,-0.036300,-0.044200,-0.041100,-0.038500,-0.042800,-0.033700,-0.042300,-0.034400,-0.033900,-0.051700,-0.040500,-0.036900,-0.048600,-0.041800,-0.041400,-0.040700,-0.045200,-0.040400,-0.046000,-0.043900,-0.055300,-0.045300,-0.035400,-0.042800,-0.039800,-0.030700,-0.032400,-0.028200,-0.039600,-0.039000,-0.035900,-0.025800,-0.030100,-0.036700,-0.014100,-0.031900,-0.026600,-0.041800,-0.031900,-0.035900,-0.011100,-0.014900,-0.027700,-0.049200,-0.027400,-0.040600,-0.032000,-0.040800,-0.0! > 42800,-0.033100,-0.044500,-0.034900,-0.048500,-0.039900,-0.035900,-0.034500,-0.032300,-0.036800,-0.044800,-0.036200,-0.020200,0.005500,-0.018100,-0.029200,-0.004300,-0.027700,-0.068300,-0.057600,-0.055700,-0.049800,-0.048900,-0.058700,0.001000,0.008700,-0.048600,0.004700,-0.049600,-0.030500,-0.059400,-0.012300,-0.013800,-0.045800,0.018700,-0.048800,-0.011000,-0.001700,0.008400,-0.023000,-0.009500,-0.059300,-0.065300,-0.008000,-0.007800,-0.018700,-0.028000,0.016300,-0.051000,-0.019800,-0.031500,0.238200,0.249400,0.216100,0.235900,0.226100,0.236800,0.209900,0.149000,0.106500,0.222100,0.197900,0.210100,0.264400,0.137800,0.134200,0.019800,-0.010000,-0.010400,0.015100,0.009800,-0.002700,0.002500,-0.005600,-0.007600,-0.016600,-0.001800,-0.005400,-0.011200,-0.002700,0.016600,0.004000,0.010300,0.003800,-0.003100,-0.027700,-0.026600,-0.040400,-0.045900,-0.017100,-0.032800,-0.030000,-0.025500,-0.045500,-0.039500,-0.037300,-0.039100,-0.029200,-0.040500,-0.027500,-0.041000,-0.041900,-0! > .046800,-0.038000,0.000400,-0.008000,-0.004200,-0.010300,-0.007400,-0. > 014600,-0.015600,-0.016800,-0.007100,-0.012600,-0.009900,-0.012400,-0.011300,-0.018300,-0.015600,-0.014800,-0.001700,-0.006000) > pgvec = c(2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2) > plot(pca1,pca2,type='p',main='Ancestry_PCA', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec) > legend("top",legend=llist,pch=glist,col=glist,title="Sample") > grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") > dev.off() > png("Ancestry_PCA_PCAPlot.pdf.png",h=8,w=10,units="in",res=72) > plot(pca1,pca2,type='p',main='Ancestry_PCA', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec) > legend("top",legend=llist,pch=glist,col=glist,title="Sample") > grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") > dev.off() > ['pdf \n', ' 2 \n', 'pdf \n', ' 2 \n'] > > ----------------------------------------------------------------------------- > job info: > None > ----------------------------------------------------------------------------- > job traceback: > None > ----------------------------------------------------------------------------- > (This is an automated message). > > -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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Re: [galaxy-dev] A tool with no inputs
by Paul-Michael Agapow 17 May '11

17 May '11

>> One of my colleagues is having trouble developing a peculiar tool: it has no inputs. This makes sense in our local >> context - it fetches some constantly updating remote data for the current user - but implementing it has escaped our >> skill. Galaxy complains about a tool with no params (i.e. an empty <inputs>). It complains about a tool with no >> <inputs> tag. Hidden input fields don't seem to work (i.e. looks like I'm getting the cached value of the form). > > From: "Duddy, John" <jduddy(a)illumina.com> > > Doesn't this violate one of the basic tenets of Galaxy - reproducibility? Without the ability to provide full > traceability to the inputs, one can make no guarantees about the outputs. I think that condition is being met - the resulting dataset depends on no inputs but the time of "fetching", and so traceability is satisfied, just like many remote and updating data sources. In any event, our pragmatic need in this case is for such a tool without any need for reproducibility. Which leads me to note the strange behaviour seen when the only input is a hidden field. When the inputs are: <inputs> <param name="input_seq_file" type="data" format="fasta" label="Input sequences" help="The sequences to have MLST profiles constructed for." /> <param name="offset" type="hidden" value="0" /> </inputs> this works as expected: a dataset selection dropdown and a hidden field (seen in the source). But if you delete the non-hidden parameter: <inputs> <param name="offset" type="hidden" value="0" /> </inputs> Galaxy doesn't generate an error, reports loading the tool, and puts an entry in the tool panel. However the link for the tool in question is malformed, missing a tool identifier and when clicked only reloads the middle welcome panel. I haven't worked out where and why this is happening, but at the least it's an uninformative error. ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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A tool with no inputs
by Paul-Michael Agapow 16 May '11

16 May '11

One of my colleagues is having trouble developing a peculiar tool: it has no inputs. This makes sense in our local context - it fetches some constantly updating remote data for the current user - but implementing it has escaped our skill. Galaxy complains about a tool with no params (i.e. an empty <inputs>). It complains about a tool with no <inputs> tag. Hidden input fields don't seem to work (i.e. looks like I'm getting the cached value of the form). It is admittedly a fairly niche use-case and we could put in a dummy field and simply not use it, but that seems inelegant. Any suggestions? ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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egg install failure: docutils, GeneTrack
by Spunde, Alex 16 May '11

16 May '11

Hi Trying to install Galaxy on local machine, using hg: hg clone http://bitbucket.org/galaxy/galaxy-dist Get error messages for two eggs: Scrambling the following eggs failed: docutils GeneTrack Here is more details for docutils (practically same for GeneTrack): [aspunde@ilmnhw-biolin10 galaxy-dist]$ python scripts/scramble.py docutils fetch_one(): Using existing source, remove to download again: /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/archive s/docutils-0.7.tar.gz unpack_source(): Removing old build directory at: /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/build/p y2.6/docutils unpack_source(): Unpacked to: /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/build/p y2.6/docutils copy_build_script(): Using build script /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/scripts /generic.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /escher/bioinfoHW/opensource/Galaxy/galaxy-dist/scripts/scramble/build/p y2.6/docutils: /escher/bioinfoHW/opensource/lib/bin/python scramble.py Traceback (most recent call last): File "scramble.py", line 29, in <module> execfile( "setup.py", globals(), locals() ) IOError: [Errno 2] No such file or directory: 'setup.py' Traceback (most recent call last): File "scripts/scramble.py", line 44, in <module> egg.scramble() File "/escher/bioinfoHW/opensource/Galaxy/galaxy-dist/lib/galaxy/eggs/scrambl e.py", line 57, in scramble self.run_scramble_script() File "/escher/bioinfoHW/opensource/Galaxy/galaxy-dist/lib/galaxy/eggs/scrambl e.py", line 206, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for docutils 0.7 Here is basic info about system: [aspunde@ilmnhw-biolin10 galaxy-dist]$ python --version Python 2.6 $ hg --version Mercurial Distributed SCM (version 1.8.3) $ uname -a Linux ilmnhw-biolin10.hwus.illumina.com 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux Thanks Alex Spunde

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