February 2016 - galaxy-dev - lists.galaxyproject.org

packaging R scripts
by Xianrong Wong 28 Feb '16

28 Feb '16

Hi, I am trying to package an R script (that requires certain R packages) into a galaxy tool. Any advice would be deeply appreciated! I have tested it on planemo and it works. When I tried the version I uploaded onto the toolshed, I got an error saying that the R packages do not exist. I next added the following lines to the R script: source("https://bioconductor.org/biocLite.R") biocLite() biocLite(c("DNAcopy", "preprocessCore")) and I got the following error when running the installed tool on galaxy: Installing package(s) ‘DNAcopy’, ‘preprocessCore’ Warning in install.packages(pkgs = doing, lib = lib, ...) : 'lib = "/usr/local/lib/R/site-library"' is not writable Error in install.packages(pkgs = doing, lib = lib, ...) : unable to install packages Calls: biocLite ... .biocLiteInstall -> .reposInstall -> install.packages Execution halted

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Docker and alpine linux
by Tiago Antao 28 Feb '16

28 Feb '16

Dear all, This email is mostly to report a negative result, maybe to help others _not_ trying something. I researched the possibility of replacing ubuntu with alpine on the Docker images (alpine seems to be used more and more on docker images, with plenty of official containers now based on it and not on debian). The reason alpine is used, its because it generates very small containers (a bare bones one is below 10 MB). But, due the the large dependencies of galaxy, the gain is negligible. Maybe 200 MB or so. 20% is something, but not a revolution. This being said, for servers with smaller dependencies (a mail server, web, ldap, dns...) alpine really reduces the footprint of docker containers. Tiago -- "While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours" - @tomstafford

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BED12 Data Format
by Lance Parsons 27 Feb '16

27 Feb '16

Does anyone know of any efforts to create a BED12 datatype for Galaxy? Since some tools require BED12 and the automatic convertion from GFF-to-BED does not seem to generate a BED12, it seems it might be a worthwhile addition. If not, what would be the best way to go about doing this? Making it part of the core galaxy (which would allow multiple tools to share the same data type definitions) or making it part of a toolshed tool (which I'm not sure how to do)? BTW, I'm thinking about RSeQC at the moment, but I know other tools use/require this format. -- Lance Parsons - Scientific Programmer Carl C. Icahn Laboratory - Room 141 (Temporary) Lewis-Sigler Institute for Integrative Genomics Princeton University

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Galaxy Docker 16.01 released!
by Björn Grüning 27 Feb '16

27 Feb '16

Hi all! We have released a new version of our Galaxy Docker Image. https://github.com/bgruening/docker-galaxy-stable https://registry.hub.docker.com/u/bgruening/galaxy-stable/ https://quay.io/repository/bgruening/galaxy A few highlights: * based on Galaxy 16.01, with all it's new awesome features * enable Travis testing for all builds and PR * offer new yaml based tool installation * documentation improvements * enable dynamic UWSGI processes and threads with -e UWSGI_PROCESSES=2 and -e UWSGI_THREADS=4 * enable dynamic Galaxy handlers -e GALAXY_HANDLER_NUMPROCS=2 * a new lite mode contributed by @kellrott * first release with Jupyter and io.bio Integration This release contains 106 commits, from 6 contributors - a big thanks to all of them! The :dev branch is already open - as usual feedback is more than welcome! Cheers, Bjoern

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GATK problems with data-manager files
by Scott Szakonyi 26 Feb '16

26 Feb '16

Hi all, One of my co-administrators is having some issues with data indexed/processed with data managers in GATK. His email to me: Currently there is no way to load a genome into versions of GATK above version 1.4. No version seems to be able to load a reference from history and only version 1.4 seems to work with the available picard-gatk data manager. We need to be able to work with these later versions of GATK, 3.4 on the Galaxy tool shed is the latest. Has anyone else experienced this sort of issue? Is there some solution for it? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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Difficulty uploading BAM files
by Scott Szakonyi 26 Feb '16

26 Feb '16

Hi, I'm having trouble uploading BAM files in our development environment. Other files types are uploading without issue. I'm testing with a small BAM file I downloaded, and I'm able to successfully upload it on our production server and usegalaxy.org. When I try to upload in the development environment, I get the following error: Traceback (most recent call last): File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 431, in <module> __main__() File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 420, in __main__ add_file( dataset, registry, json_file, output_path ) File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line 347, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 218, in dataset_content_needs_grooming version = self._get_samtools_version() File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 179, in _get_samtools_version raise Exception(message) Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH. I've checked my installed tools, and all the same Samtools packages are successfully installed on the development environment as in production. I don't see any missing dependencies or anything like that. At this point I'm stumped. If anyone can offer some guidance on how to resolve this, I'd be most appreciative. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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Issue with Using Bar
by Harrison Thompson 26 Feb '16

26 Feb '16

Hello, I am using Galaxy for a school project, but I’m running into an issue with my “Using Bar” in the top right corner. I started off running programs at roughly 30% using. I then downloaded a number of sequences to analyze and went above 100% on my Using Bar. I then purged the entirety of my history and still am at 80+% of my Using Bar. Is there something I’m not deleting that I need to? I really need it to go down to run my class project, but I’ve tried deleting everything, and it’s not working. Thanks, Harrison hmt0003

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samtools view tools
by Christian Brenninkmeijer 26 Feb '16

26 Feb '16

Hi All, Has anyone written galaxy tools for the samtools view functions such as samtools view -f 0x0002 -F 0x0100 -uo and/or samtools view -uSo Thanks Christian University of Manchester

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Seeking Job Metrics Clarity
by Ziphozakhe Mashologu 26 Feb '16

26 Feb '16

Hi All I have enabled job metrics on a local galaxy install, with latest code from dev branch. I have "<collectl /> " uncommented in job_metrics_conf.xml file: Following are the errors in the logs: galaxy.jobs.metrics ERROR 2016-02-24 12:28:08,741 Failed to collect job properties for plugin <galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin object at 0x7ff0b6af3a50> Traceback (most recent call last): File "dev/galaxy/lib/galaxy/jobs/metrics/__init__.py", line 101, in collect_properties properties = plugin.job_properties( job_id, job_directory ) File "dev/galaxy/lib/galaxy/jobs/metrics/instrumenters/collectl.py", line 105, in job_properties raise Exception( message ) Exception: Failed to find collectl log in directory It seems like collectl is looking for the following files: ['__instrument_collectl_pid', '__instrument_env_vars', 'galaxy.json', 'metadata_kwds_HistoryDatasetAssociation_2_1rh1WC', 'set_metadata_N05Q24.py', '__instrument_core_galaxy_slots', 'metadata_results_HistoryDatasetAssociation_2_33gTDj', '__instrument_core_epoch_start', 'galaxy_2.sh', 'metadata_out_HistoryDatasetAssociation_2_G5bZYP', '__instrument_core_epoch_end', '__instrument_meminfo_meminfo', '__instrument_uname_uname', 'metadata_override_HistoryDatasetAssociation_2_krldDM', 'set_metadata_lpIXS5.py', 'metadata_in_HistoryDatasetAssociation_2_iiYW0t', '__instrument_cpuinfo_cpuinfo', 'tool_script.sh', 'galaxy_2.ec'] Which are suppose to exist under galaxy/database/job_working_directory/000 job directory. Has anybody faced anything similar issue or is it a configuration issue, or perhaps a known issue with job_metrics (collectl)? BTW: I installed collectl packages on the host. Regards Zipho

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Re: [galaxy-dev] JBrowse on dev branch: progress
by Peter van Heusden 26 Feb '16

26 Feb '16

Thanks Peter I managed, on the second attempt, to get past the gnu coreutils problem. Zipho noticed a weird lockup though: conftest that seemed to be from the gnu coreutils install wanted to listen on port 4001, which is the same port our uwsgi server listens on. The install has now completed but I'll try and find time to go back and verify this. On the second attempt perl seems to be installing, so I'll see if it completes or hits the error you're mentioning. Peter On 22 February 2016 at 11:34, Peter Briggs <peter.briggs(a)manchester.ac.uk> wrote: > Hi Peter > > I think that package_perl_5_18 in the tool shed is broken, I came across > the same error last week on both our production instance and a local 'test' > instance (both v15.10). > > My suspicion is that the following lines are to blame: > > ... > <action > sha256sum="5c69adb47ab828aa3e8b5be89b88cd49c6a0d0dae2e8b3bca17a9ce699190e7b" > type="download_file"> > http://www.cpan.org/authors/id/A/AP/APEIRON/local-lib-1.008009.tar.gz > </action> > <action type="shell_command">tar xfvz > local-lib-1.008009.tar.gz</action> > ... > > Looking at the Galaxy internals I believe that the 'download_file' action > automatically unpacks the archive and cd's into the resulting directory, > hence the failure for the subsequent 'tar xfvz ...' command. But I haven't > had the time yet to verify this or create a patch to see if the removal of > this line addresses the problem. > > I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that > you describe however so it may be that my hypothesis is not correct. > > HTH > > Best wishes > > Peter > > > On 22/02/16 05:10, Peter van Heusden wrote: > >> Hi there Eric and others >> >> I tried to install the JBrowse tool on a dev branch server running on an >> Ubuntu 14.04 VM. >> >> It got stuck at the package_gnu_coreutils_8_22 dependency (revision >> ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state. >> >> If I go look at the tool details it highlights errors >> in package_perl_5_18 which in turn refers to errors in gnu_coreutils >> (just "Error" state) and then this more informative failure for perl: >> >> "tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or >> directory >> tar (child): Error is not recoverable: exiting now >> tar: Child returned status 2 >> tar: Error is not recoverable: exiting now" >> >> I wonder if this is a sign of a download error? >> >> Digging a bit more I find the error "Shutting down process id 21094 >> because it generated no output for the defined timeout period of 3600.0 >> seconds." for gnu_coreutils. >> >> I'm trying to do a reinstall of the gnu_coreutils and perl packages to >> see if I can get further. >> >> Peter >> >> >> ___________________________________________________________ >> 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/ >> >> > -- > 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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