galaxy-dev January 2016

galaxy-dev@lists.galaxyproject.org

59 participants
80 discussions

Bowtie2
by Laforest, Martin 13 Jan '16

13 Jan '16

Hello, Please excuse my simple question since I'm a newbie... I've searched the mailing list but did not find the appropriate answer... I have a new Galaxy installation. I installed the tool "Bowtie2: Fast and sensitive read alignment" (Revision 019c2a81547a, Owner: devteam). The tool apparently runs fine and I can download the BAM file at the end and see its content (with IGV for example). The problem is that my dataset is red and when I check the error, I get "OSError: [Errno 2] No such file or directory"... Maybe it is when Galaxy tries to set the data type, I don't know. Many thanks for your help. Martin

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tools to reduce list of datasets.
by Christian Brenninkmeijer 13 Jan '16

13 Jan '16

Hi All, Can someone point me to documentations/ examples of how to write a tool to reduce a a list of datasets back into a single dataset. == What I want to do is process multiple pairs of reads. 1. load all the fastq files. 2. create a list of pairs 3. Run tools of each pair in the list (As a seperate job for each pair) 4. Run a single tool over all the results of 3 at the same time! (One job which takes all the files/ whole collection) as input. thanks in advance Christian

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Please terminate iGeneMap cluster
by Laura Song 12 Jan '16

12 Jan '16

Hi, I accidentally launched iGeneMap cluster. Please help me terminate it. Thanks. Laura

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11 Jan '16

Hi All, I tried to turn on login required in config.ini But now if you are not logged in it loads the main page where normally the welcome.html would go. Which then recursively loads other main pages. Which file am I missing? Thanks Christian University of Manchester

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Job metrics configuration
by Peter van Heusden 11 Jan '16

11 Jan '16

Hi there I'm trying to understand how the job metrics configuration works. Reading through various examples, it looks like it works together with the dynamic destination support. First on the dynamic destination support, this works, as I understand it, by importing modules (files ending in .py) from the directory set as the rules_module, where rules_module is a parameter for the dynamic job plugin. As in this snipped from the usegalaxy configuration: <plugin id="dynamic" type="runner">  <param id="rules_module">usegalaxy.jobs.rules</param> </plugin> So import usegalaxy.jobs.rules, find where this resolves to as a directory, find all .py files in that directory. If rules_module is not specified, the default is galaxy.jobs.rules (under galaxy/lib). So these .py files are imported and within them are functions that are used in dynamic destinations (those with runner="dynamic") and in turn tools are directed to use these destinations. Now the job metrics configuration supplies both a user interface and then a set of keys that are made accessible to dynamic runners as key value pairs on the job.parameters attribute (passed in as the third argument, i.e. job). Specifically the job metrics configuration exists under a key '__job_resource'. Is this all correct? Is there a more straightforward way of moving from job resource specification to job configuration than this? Thanks, Peter

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running in job_working_directory
by Jorrit Boekel 11 Jan '16

11 Jan '16

Dear all, I (finally) started transitioning our lab’s tools from using parallelism (the multi-splitter) towards collections. In the parallelism scenario, tools were run in their respective working dir, resulting from a chdir performed in extract_parts.sh. That was nice. But I see when using collections that there is a workdir around, but the tool is not actually run in it. I often need to symlink to change input file extensions and can’t imagine noone else does that, so I wondered if I was missing something. If I’m not, then here’s my two questions: - Is there an accepted place to symlink files in (and how do I pass the working dir in a tool XML)? I don’t want them in the files/ dir, looks bad, they’re not cleaned, etc etc. - Would it be a bad idea to make tools run inside a workdir, apart from possibly breaking backwards compatibility? cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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Some workflows not scheduled until handler restart
by Jelle Scholtalbers 08 Jan '16

08 Jan '16

Hi all, On our installation (v15.07) we suddenly see that one of two job handlers get stuck with a high cpu load (last message generally, `cleaning up external metadata files`) without new messages appearing. In addition, when running workflows in batch (>6x), only a few of them (~3) get their workflow steps/jobs scheduled (LSF-DRMAA). For the remaining 3, their new histories are created but remain empty (according to the GUI). Only upon restart of the two job handlers the remaining workflow steps are scheduled and shown in the history. First question, how do we resolve this issue? Second, how does this actually work? How are the workflow steps stored in the database i.e. why are they not shown in the web interface until they are processed by a handler? Possible relevant config settings: [server:handler0] use_threadpool = true threadpool_workers = 5 [server:handler1] use_threadpool = true threadpool_workers = 5 [app:main] force_beta_workflow_scheduled_min_steps=1 force_beta_workflow_scheduled_for_collections=True track_jobs_in_database = True enable_job_recovery = True retry_metadata_internally = False cache_user_job_count = True # only a limit set for the very few local tools like upload Cheers, Jelle

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Extract features : error loading field data in usegalaxy
by Gildas Le Corguillé 08 Jan '16

08 Jan '16

Hi, One of my user wanted to import a workflow using the tool "Extract features" provided in the galaxy distrib : tools/filters/gff/extract_GFF_Features.xml On my instance, in the workflow canevas, I get this in red "error loading field data" On usegalaxy.org, I happy to observe that it's the same ... Sorry :) Any idea ? Gildas -- ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and Bioinformatics for Marine Science) Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 http://abims.sb-roscoff.fr ------------------------------------------------------------------

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Interactive Environment on a VM
by Mic 07 Jan '16

07 Jan '16

Hello, Does anyone has a VM with working Interactive Environment (Rstudio and Ipythyon)? A VM would possible solve the problem with Docker-in-Docker issues ( https://github.com/bgruening/docker-galaxy-stable/issues/127 & https://github.com/docker/docker/issues/19114#issuecomment-169329721 ). Thank you in advance. Mic

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Apache proxy and sub-directory setting of local galaxy
by XiaoTao Jiang 07 Jan '16

07 Jan '16

Dear Sir I set up my local Galaxy with Apache proxy according to document https://wiki.galaxyproject.org/Admin/Config/ApacheProxy This work for my website only if I take the port number 8080 with my domian name. If I remove the port, it does not work. I am new to Galaxy, is there anyone can find out the problem of my settings? With port it is work [image: 内嵌图片 1] Without it does not work [image: 内嵌图片 2] My Apache configure file for galaxy is like this *conf.d/galaxy-dev.conf* [image: 内嵌图片 3] my universe_wsgi.ini configuration for port [image: 内嵌图片 4] [image: 内嵌图片 5] [image: 内嵌图片 6] Any suggestions are welcome, thanks in advance for your help. Regards Xiao-Tao Jiang -- Regards, Xiao-Tao Jiang Department of Engineering The University of HongKong

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galaxy-dev January 2016