galaxy-dev March 2016

galaxy-dev@lists.galaxyproject.org

74 participants
98 discussions

planemo update failing on testtoolshed
by Peter van Heusden 18 Mar '16

18 Mar '16

Hi there I'm trying to update a newly created tool on the test tool shed and I get this error: $ planemo shed_update -t testtoolshed cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git rev-parse HEAD cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git diff --quiet Could not update split_fasta_chunks Unexpected response from galaxy: 500: <html> <head><title>Internal Server Error</title></head> <body> <h1>Internal Server Error</h1> <p>The server has either erred or is incapable of performing the requested operation. <br/> </p> <hr noshade> <div align="right">WSGI Server</div> </body> </html> Repository metadata updated. Failed to update a repository. I might have accidentally created a "bad" repository that is leading to this error. This is with version 0.23.0. Alternately, is there a way to delete the tool so that I can try and recreate it? Thanks! Peter

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removing tool from toolshed
by Xianrong Wong 18 Mar '16

18 Mar '16

Hi, I've recently packaged some of my scripts and deposited them into the test toolshed. Are there ways to remove some of them ie remove the repository completely? Jose

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Cloudman & AWS IAM_PROFILE support?
by Ryan G 17 Mar '16

17 Mar '16

Hi - Does Cloudman support IAM_PROFILES? We run our instances within a VPC and assign an IAM_PROFILE to the ec2 instances so that they have access to resouces. Does Cloudman have this support?

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Test tool shed api - repositories.get_ordered_installable_revisions() not working?
by Simon Gladman 17 Mar '16

17 Mar '16

Hi all, I've been trying to access the test tool shed via the bioblend api. It keeps failing when I try to call get_ordered_installable_revisions() on a connection to it. Is anyone else having this problem. Please find a jupyter screenshot where I have replicated this problem. It all works fine on the main toolshed. [image: Inline images 1] -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 700 Swanston Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.gladman(a)unimelb.edu.au Web: http://www.vlsci.org.au

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Re: [galaxy-dev] Please help fix toolshed repository: trtr
by Martin Čech 17 Mar '16

17 Mar '16

Hi Lance, Dave Bouvier removed the unwanted folder on the TS side. (It wasn't ever tracked by mercurial). You should be ok now. Sorry for the inconvenience. Thank you for using Galaxy. Martin On Tue, Mar 15, 2016 at 5:41 PM Lance Parsons <lparsons(a)princeton.edu> wrote: > When I clone the repo, I don't see that folder: > > hg clone https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr > > Lance > > Martin Čech wrote: > > > Hi Lance, > > it seems the whole .git/ folder got accidentally uploaded there and it > causes trouble. I recommend using the direct mercurial access > (https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr), delete the > folder, commit the change and push it to the TS repository. > > Please let me know how it goes. > > Martin > > On Tue, Mar 15, 2016 at 4:54 PM Lance Parsons <lparsons(a)princeton.edu > > <mailto:lparsons@princeton.edu>> wrote: > > I was helping someone with their toolshed repository and we ran > into an issue, there is an old folder "myTools" in the repository > that we cannot delete. It has a second copy of the tool > (inadvertently). However, when we upload a new version with > Planemo, the directory remains. Attempts to delete it via the > toolshed web interface result in internal server errors. Can an > admin take a look? > > https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301 > > > -- > Lance Parsons - Scientific Programmer > Carl C. Icahn Laboratory - Room 136 > Lewis-Sigler Institute for Integrative Genomics > Princeton University > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > >

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Re: [galaxy-dev] Scaling tools: data available? (Peter van Heusden)
by Dooley, Damion 17 Mar '16

17 Mar '16

If you are looking for a simple python program to log cpu% and memory of another executable, then analyze.py might do. Its in https://github.com/Public-Health-Bioinformatics/kipper/tree/master/RDP-test -case along with a few scripts that show examples of its use. Damion >> >> On 02/21/2016 11:13 PM, Peter van Heusden wrote: >> >> Hi there >> >> We're researching the resource (CPU time and memory) requirements for >>RNA >> STAR at the moment. Specifically, we'd like to build up a database of >>input >> size to resource usage so that we can use this to feed a dynamic >> destination mapper (currently our STAR configuration uses a thumbsuck >>for >> RAM and CPU requirements that is not optimal but works in many cases). >> >> Has anyone collected these metrics before? And more generally, is anyone >> collecting metrics for a range of bioinformatics tools? A database like >> this could be very useful! >> >> Thanks! >> Peter >>

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Announcement: Galaxy DevOps Workshop
by Bjoern Gruening 17 Mar '16

17 Mar '16

Hi all, We would like to invite you to our Galaxy DevOps Workshop in Heidelberg from 6-7 of April, organised by de.NBI and ELIXIR. The workshop is intended for Bioinformaticians who want to * learn the internals of the multi-omics Galaxy workbench * learn how to set up and run a Galaxy server * learn about Galaxy tool development * get questions answered from experienced Galaxy admins and community members * are interested in reproducible and accessible research For more information please see https://goo.gl/8dNSdy Ciao, Bjoern

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Using forms to collect user info at registration
by Peter Briggs 17 Mar '16

17 Mar '16

Hello I'm trying to set up a form within Galaxy to collect some user info at registration time. The only documentation I've found on this functionality is: https://wiki.galaxyproject.org/Admin/Config/User%20Information which seems to be precisely what I need. However I can't make this work as described. When I set up a form and then go to the registration page, instead of the additional form options I get a single field called "User type" with a drop-down menu widget with a single option ("User registration form" i.e. the name of the form that I created). I've looked to see if there is a config option to turn something on, or if I need to create a role, but so far nothing I've tried seems to make a difference. Does anyone have any suggestions on how I might get this feature to operate as advertised? (Btw I'm seeing this in both 15.10 and 16.01.) Thanks for your help, Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Galaxy drops my tenth xml tool parameter
by rbrown1422＠comcast.net 16 Mar '16

16 Mar '16

Good afternoon, It appears my Galaxy updated overnight and has caused issues that I am fairly certain I didn't introduce. Did something change or what did I do? 1 the Parameter $GALAXY_ROOT_DIR/tools/Heatmaps/' is not showing up see bottom where I dump parameters. 2. The repeat seems to always run once even when I do not click and fill it. This was working a couple days ago. I was playing with it - but very minimally-- yeah i understand but have worked with Galaxy for awhile. Thanks Bob 3. <?xml version="1.0" encoding="UTF-8" ?><tool id="heatmap" name="Heatmap" version="3.1.1"> <description>Create HeatMap </description><command>$GALAXY_ROOT_DIR/tools/MDA_Heatmaps/heatmap.sh '$hmname' '$hmdesc' '$inputmatrix' $rowOrderMethod $rowDistanceMeasure $rowAgglomerationMethod $columnOrderMethod $columnDistanceMeasure $columnAgglomerationMethod '$summarymethod' '$GALAXY_ROOT_DIR/tools/Heatmaps/' #for $op in $operations ${op.class_name} ${op.repeatinput.file_name} ${op.cat} #end for '$output' </command> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <inputs> <param name="hmname" size="20" type="text" value="HM_name" label="User Defined HeatMap Name"/> <param name="hmdesc" size="100" optional="true" type="text" value="_" label="Optional HeatMap Description"/> <param name="inputmatrix" type="data" label="Input Matrix" /> <param name="summarymethod" type="select" label="Data Summarization Method"> <option value="average">average</option> <option value="sample">sample</option> <option value="mode">mode</option> </param> <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> <option value="HierarchicalClustering">Hierarchical Clustering</option> <option value="OriginalOrder">Original Order</option> <option value="Random">Random</option> </param> <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation"> <option value="euclidean">Euclidean</option> <option value="binary">Binary</option> <option value="manhattan">Manhattan</option> </param> <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'."> <option value="average">Average Linkage</option> <option value="complete">Complete Linkage</option> <option value="single">Single Linkage</option> </param> <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random"> <option value="HierarchicalClustering">Hierarchical Clustering</option> <option value="OriginalOrder">Original Order</option> <option value="Random">Random</option> </param> <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation"> <option value="euclidean">Euclidean</option> <option value="binary">Binary</option> <option value="manhattan">Manhattan</option> <option value="correlation">Correlation</option> </param> <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'."> <option value="average">Average Linkage</option> <option value="complete">Complete Linkage</option> <option value="single">Single Linkage</option> <option value="ward">Ward</option> <option value="mcquitty">Mcquitty</option> <option value="median">Median</option> <option value="centroid">Centroid</option> </param> <repeat name="operations" title="Covariate Bars"> <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name"/> <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/> <param name="cat" type="select" label="Axis Covariate Type"> <option value="row_categorical" >row categorical</option> <option value="row_continuous" >row continuous</option> <option value="column_categorical" >column categorical</option> <option value="column_continuous" >column continuous</option> </param> </repeat> </inputs> <outputs> <data name="output" label="${inputmatrix.name}_Heatmap" format="zip"/> </outputs></tool> 4. dump of part of heatmap.sh commands echo $1 $2 $3 $4 $5 $6 $7 $8 $9 $10echo 11-14 belowecho $11 $12 $13 $14 5. shows in Stdout the 10th parameter '$GALAXY_ROOT_DIR/tools/Heatmaps/' is missing The first 10 params are: namexyz test /home/rbrown/HM_galaxy/database/files/000/dataset_500.dat HierarchicalClustering euclidean average HierarchicalClustering euclidean average namexyz0 11-14 below namexyz1 namexyz2 namexyz3 namexyz47. and where do the namexyzN come from? I didn't click the repeat -- yes one of them should by file Output

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Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)
by Peter Briggs 16 Mar '16

16 Mar '16

Hello I've encountered an issue with running the cuffdiff tool on our local production Galaxy instance. Specifically when a cummerbund SQLite database is requested as output then the tool fails with an error: Creating database ./cummeRbund.sqlite Error in sqliteSendQuery(con, statement, bind.data) : error in statement: disk I/O error Error in sqliteSendQuery(con, statement, bind.data) : error in statement: disk I/O error Calls: readCufflinks ... .local -> sqliteGetQuery -> sqliteSendQuery -> .Call Execution halted Our Galaxy is configured to use a LustreFS scratch directory for the 'job_working_directory', which I understand is where each job will have its own working directory created, and I'm wondering if the SQLite error above is a manifestation of a general problem with SQLite on LustreFS (see e.g. the answer to this BioStars question https://www.biostars.org/p/115452/). The obvious workaround is to change 'job_working_directory', preferably just for the cuffdiff tool. Does anyone know if it's possible to do this i.e. set 'job_working_directory' on a per-tool basis? (Also, has anyone else seen this specific problem with cuffdiff/cummerbund/SQLite on their local Galaxy instances?) Thanks for your help - any suggestions greatly appreciated, Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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galaxy-dev March 2016