Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
Hi Thon double check your datatypes_conf.xml (which was not touched/changed during the update process, since it is listed in the .hgignore file, I guess) with the new datatypes_conf.xml.sample file for any changes regarding converters for bed files Regards, Hans-Rudolf On 08/22/2013 02:51 AM, Anthonius deBoer wrote: Yep... $ bedtools --version bedtools v2.17.0 Thon On Aug 21, 2013, at 01:40 PM, sam guerler aysam.guer...@gmail.com wrote: Hi Anthonius, Do you have the BEDTools installed and its directory added to your PATH environment variable? Trackster uses compressed file formats to reduce the amount of data transfers. I hope this helps, Sam On Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer thondeb...@me.com mailto:thondeb...@me.com wrote: Hi, I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check my datatypes_conf.xml which I did (not sure what I should be looking for, but this is the section on BED files... Am I missing a converter? And why would a BED file even needed to be converted? Thanks Thon datatype extension=bed type=galaxy.datatypes.interval:Bed display_in_upload=true converter file=bed_to_gff_converter.xml target_datatype=gff/ converter file=interval_to_coverage.xml target_datatype=coverage/ converter file=bed_to_bgzip_converter.xml target_datatype=bgzip/ converter file=bed_to_tabix_converter.xml target_datatype=tabix depends_on=bgzip/ converter file=bed_to_summary_tree_converter.xml target_datatype=summary_tree/ converter file=bed_to_fli_converter.xml target_datatype=fli/ !-- display file=ucsc/interval_as_bed.xml / -- !-- display file=genetrack.xml / -- display file=igb/bed.xml / /datatype datatype extension=bedgraph type=galaxy.datatypes.interval:BedGraph display_in_upload=true converter file=bedgraph_to_bigwig_converter.xml target_datatype=bigwig/ /datatype datatype extension=bedstrict type=galaxy.datatypes.interval:BedStrict / !-- datatype extension=bed6 type=galaxy.datatypes.interval:Bed6 converter file=bed_to_genetrack_converter.xml target_datatype=genetrack/ /datatype -- datatype extension=bed12 type=galaxy.datatypes.interval:Bed12 / datatype extension=len type=galaxy.datatypes.chrominfo:ChromInfo display_in_upload=true converter file=len_to_linecount.xml target_datatype=linecount / /datatype datatype extension=bigbed type=galaxy.datatypes.binary:BigBed mimetype=application/octet-stream dis ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Release Cycle Length
Hi Dave, I am one of the requesters on a less frequent release. Certainly this does not need to replace the current release scheme in the development branch: Galaxy system users who prefer keeping their code up to date can still go there. It is just nice to have a separate branch with a less frequent stable release cycle with the support of fixing major bugs as Hans-Rudolf pointed out. This fixing support is only needed on the latest stable release. Regarding the frequency of such a release, I would say it is a bit dependent on the speed of introducing new major features in Galaxy. I wouldn't mind to have a 4 or 6 month release cycle in the stable branch if they synchronize better with the major milestones in Galaxy. Thanks, Leon Message: 3 Date: Wed, 21 Aug 2013 08:57:22 +0200 From: Hans-Rudolf Hotz h...@fmi.ch To: Dave Clements cleme...@galaxyproject.org Cc: Galaxy Dev List galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Galaxy Release Cycle Length Message-ID: 521464d2.5010...@fmi.ch Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Dave two months is a good time between releases. Much more important than the release cycle length is fixing identified bugs on the release branch as well. Regards, Hans-Rudolf On 08/20/2013 08:36 PM, Dave Clements wrote: Hello all, At one of the GCC2013 Birds of a Feather sessions http://wiki.galaxyproject.org/Events/GCC2013/BoF/PublicGalaxyServers the group was very clear that they would like to see less frequent releases of Galaxy. We're currently aiming to do a release every 2 months and have been pretty successful at making that target. In the past, we have tried doing releases more often and less often. Is there a sweet spot for the time between releases? Please reply to the group. We are interested in a discussion. Thanks, Dave C -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nlhttps://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_meiMobile: +31 6 41709231 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] developing a tool which could encapsulate any tool
On Thu, Aug 22, 2013 at 4:14 PM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi All, I am trying to develop a generic Galaxy tool which could encapsulate any other Galaxy tool and run it. The motivation behind this development is to enable running ordinary Galaxy tools in parallel with multiple datasets and/or running ordinary tools on large-scale compute resources. I was wondering about the Galaxy-way of doing this. Is there a natural pattern I could adapt here for this work? Are there any existing examples which does this? Hi Ketan. This is a little broader than your initial question, http://lists.bx.psu.edu/pipermail/galaxy-user/2013-August/006511.html There has been a lot of work done already on running Galaxy on multiple datasets at once - some of which is already built into Galaxy, while other like John Chilton's multiple-file support is only available as an experimental branch, e.g. http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-December/012265.html https://bitbucket.org/msiappdev/galaxy-extras/src/extras/README_EXTRAS.txt Galaxy also has the capability to split large jobs into many parts to take advantage of a cluster - I use this in the BLAST+ wrapper to break up searches into batches of 1000 queries for example. This isn't enabled by default, but we're using in on our instance. Regards, 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Passing user_email to a data source
Hi, I have written a patch for this. The pull request is there : https://bitbucket.org/galaxy/galaxy-central/pull-request/206/give-access-to-__user_email__-and It works fine on my galaxy instance. Cheers Anthony On 21/08/2013 08:51, Hans-Rudolf Hotz wrote: Hi Anthony I doubt it will solve your problem, but just as a general hint: you can use the email address for filtering. In our case, the user gets a different list of groups he/she can select from, eg: param name=group type=select label=Select your group options from_file=access_to_miseq column name=email index=0/ column name=value index=1/ filter type=static_value name=external_source_filter value=$__user_email__ column=0/ /options /param and our file '~/tool-data/access_to_miseq' looks like: 1...@fmi.chgbioinfo 1...@fmi.chgfungen 1...@fmi.chgmeier ## a...@fmi.chgfungen ## 1...@fmi.chgfungen 1...@fmi.chgmeier Regards, Hans-Rudolf On 08/20/2013 05:51 PM, Anthony Bretaudeau wrote: Hello, I'm trying to add a new data source to my Galaxy instance, using synchronous data depositing. The data source needs to know the email address of the user who tries to import data to the Galaxy server. I would have like to write something like that: inputs action=https://example.com/my/data/source; check_values=false method=get displayBrowse the XX data source $GALAXY_URL/display param name=user_email type=hidden value=$__user_email__ / /inputs Then Galaxy would have generated this url: https://example.com/my/data/source?GALAXY_URL=httpuser_email=t...@example.com But this doesn't work, because the $__user_email__ seems to be available only in command tag. I end up with this url which is useless: https://example.com/my/data/source?GALAXY_URL=httpuser_email=$__user_email__ Is there any way to do what I need to do? It would be great if variables were available in param tags too. Otherwise, maybe I could write a custom tool type to do this. Is there any guideline for this? I have seen someone talking about that a few months ago, but with no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011258.html Thanks for your help Regards Anthony Bretaudeau ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
