December 2012 - galaxy-dev - lists.galaxyproject.org

Tool dependency installation fail, any documentation?
by Franco Caramia 12 Dec '12

12 Dec '12

Hi list, I got the following tool_dependencies.xml file failing: <?xml version="1.0"?> <tool_dependency> <package name="bedtools" version="2.17.0"> <install version="1.0"> <actions> <action type="download_by_url" target_filename="bedtools-2.17.0.tar. gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> <action type="shell_command">make clean</action> <action type="shell_command">make all</action> <action type="move_directory_files"> <source_directory>bin</source_directory> <destination_directory>$INSTALL_DIR/bin</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DI R/bin</environment_variable> </action> </actions> </install> <readme> GCC version 4.1 or greater is recommended. 3.x versions will typically not c ompile BEDTools </readme> </package> </tool_dependency> The error given is: ############################################# make clean STDOUT ############################################# ############################################# make clean STDERR make: *** No rule to make target clean'. Stop. ############################################# I basically just copied the example code from the Galaxy wiki for R: <?xml version="1.0"?> <tool_dependency> <set_environment version="1.0"> <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> <package name="R" version="2.15.1"> <install version="1.0"> <actions> <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.g z</action> <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> <action type="shell_command">make</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. </readme> </package> </tool_dependency> I have found no documentation to what the tag <action type="download_by_url"> does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn¹t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance... Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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"Delete Permanently" problem
by Fenglou Mao 12 Dec '12

12 Dec '12

I installed a local galaxy server, did some calculation. Now I want to clean datasets for some space. I tried "Delete Permanently" on both datasets and histories, none of them worked. The datasets and histories will be marked as "deleted", but it will not be really deleted even I am using "Delete Permanently". They will not be really removed, and space are not released. Sometimes it will give me a message "this feature is not enabled", sometimes it won't. Any one know how to enable "Delete Permanently" feature? Thanks, Fenglou

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Re: [galaxy-dev] help on galaxy on the cloud
by Enis Afgan 12 Dec '12

12 Dec '12

Hi Alfonso, How did you launch your instance? Did you try using http://usegalaxy.org/cloudlaunch If not, give that a shot and see if you get up and going fine. If not, please send another email and we'll figure it out there. (I've CC-d galaxy-dev mailing list, which is the best place to get help on these topics.) Cheers, Enis On Thu, Dec 13, 2012 at 5:12 AM, Alfonso Garrido-Lecca < Alfonso.Garrido-lecca(a)colorado.edu> wrote: > Hello Enis, > I am a post-doc in the Blumenthal lab in Boulder, Colorado, US. > I been trying to set galaxy on the cloud on the lab, but I am experiencing > some > difficulties connecting with the galaxy interface. > When you have a chance could you please let me know who could help me on > this? > please let me know, > thanks, > Alfonso >

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How to add to add hg16 index into the build-in index / reference gnome list?
by Sachit Adhikari 12 Dec '12

12 Dec '12

How do I add hg16 into the build-in index?

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Questions about Install GATK on local instance
by ygong＠cpdr.org 12 Dec '12

12 Dec '12

Hi, all, I'm installing GATK on galaxy local instance now and I have some questions may need your help. I downloaded the GATK2 from GATK website htt http://www.broadinstitute.org/gatk/download . the link is http://www.broadinstitute.org/gatk/auth?package=GATK I knew that on galaxy tool dependencies page http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies they gave the link for GATK 1.4 version but I can't figure out how to download and install it, and I noticed that GATK2 have all 1.x version features, so I installed GATK2. In the GATK 1.4 link (https://github.com/broadgsa/gatk ) that shown on http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, there are multiple folders and files and I got really confused what I need to download. Even I choose "ZIP" to download a zip file, I counld not figure out whether it is the program package and don't know how to install it. Maybe this is the problem. But based on my understanding, GATK is just a set of java package, and all we need to do is put it into /tool-data/shared/jars folder, right? That is how I did it for GATK2. The GATK2 package include a folder called "resources" and a file called "GenomeAnalysisTK.jar" . I put them into /tool-data/shared/jars/gatk folder. I tested the installation following the instruction : http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-… And I request a key from broadinstitute and followed the instruction on http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… But the galaxy still gave me the error message as followed： ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… for more information and instructions on how to obtain a key. ##### ERROR ------------------------------------------------------------------------------------------ I guess I may made mistakes in some point: 1. I should not install GATK2 but only GATK 1.4 so that Galaxy can use it. But I really don't know how to download and install it. I can't find the correct file. 2. GATK2 works on Galaxy but I did something wrong on installing it. Could anyone help me about this? It will be greatly appreciated. Thanks. Anthonel

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Working directly with gzipped files
by Fabiano Lucchese 12 Dec '12

12 Dec '12

Hi, all. I set up a local installation of Galaxy and have been trying to reproduce inside it what I had previously accomplished with command-line scripts. One of the tools that I'm using is BWA, so I installed the "Map with BWA Illumina" tool from the tool shed. So far so good. However, when performing alignments at the command-line, I was able to directly input fastq.gz files onto BWA, which doesn`t seem to be possible inside Galaxy. Besides saving a lot of storage space, working with gzipped fastq files turned out to give me faster results too, so it's a "must have" feature for me. When I try to create a BWA task, the form complains that there isn`t any compatible file in my history. If I try to see the files contents, there's an error message complaining about their encoding. If I gunzip the files, everything works fine. Am I falling into any beginner's dumbness? Thanks in advance. F.

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Extra files saved outside of Galaxy's history?
by Gomez, Ann 12 Dec '12

12 Dec '12

Hi all, I have a pipeline involving a series of scripts, which creates directories (and many subdirectories), that I'd like to wrap for use in Galaxy. Although the contents of the folders are not the primary output of the pipeline, (and I don't want them as history items), I'd still like them to be accessible for users to double-check the contents if they so desire. However, I'm not sure where a good place to create/persist the folders would be. Although I'm running a local install on my own machine for the moment, the goal will be to move to a cluster in the near future. Does anyone have experience with this kind of thing or have any ideas? Apologies if I've missed something; I haven't found anything related on the mailing list or the wiki, except for this thread that suggests disabling the cleanup method of the JobWrapper for debugging purposes: http://dev.list.galaxyproject.org/persisting-job-working-directory-td413 8922.html. Thanks for your consideration, Ann

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some problem with the fastq interlacer
by 泽蔡 12 Dec '12

12 Dec '12

Hi all, I ran the fastq interlacer with a fastq encoding 1.8+ data, the interlacer seems do not reganize the name of the pair-end reads, and treat the pair-end reads as non-pair-edn reads. Best regards

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pbs_python and torque 4.x
by Steve.Mcmahon＠csiro.au 11 Dec '12

11 Dec '12

Hi all, We are trying to get our instance of Galaxy submitting jobs to a cluster a using the staged method referred to at http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster. Our cluster is running Torque 4.1.3. We need to use Torque 4.x clients to be able to submit jobs to it. I've set up our Galaxy server to be able to submit jobs and stage data in and out. Galaxy can't submit jobs to the cluster, however. The problem seems to be with pbs_python. On the associated wiki there is a ticket for the problem and I have been able to reproduce it. https://oss.trac.sara.nl/pbs_python/ticket/31 Has anyone had any experience with getting pbs_python to work with Torque 4.x? Regards. Steve McMahon Solutions architect & senior systems administrator ASC Cluster Services Information Management & Technology (IM&T) CSIRO Phone: +61-2-62142968 | Mobile: +61-4-00779318 steve.mcmahon(a)csiro.au<mailto:steve.mcmahon@csiro.au> | www.csiro.au<http://www.csiro.au/> PO Box 225, DICKSON ACT 2602 1 Wilf Crane Crescent, Yarralumla ACT 2600

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Galaxy doesn't detect the file when we add dataset to a library under Manage data libraries
by Sachit Adhikari 11 Dec '12

11 Dec '12

Hi list, We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select "Copy file into Galaxy" under "Copy data into Galaxy?" option and does not detect it when we select "Link to files ..." Is this a known issue? If it is, is there any workaround to solve the issue? Thanks Regards, Sachit

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