- galaxy-dev - lists.galaxyproject.org

potential operate on genomic intervals-intersect bug
by Michael Wilson 28 Aug '12

28 Aug '12

Dear Galaxy, Last night (1AM) and today (10:45AM) I have not been able to return results with the operate on genomic intervals, intersect tool. For example if I upload ChIP-seq peak replicates in .gz format (downloaded directly from ENCODE), no results are returned when they are intersected with each other (or with themselves). If I use the Join tool I indeed am able to join many intervals as would be expected. Not sure if I am doing something wrong this time..... Here is a shared history link to give an example: https://main.g2.bx.psu.edu/u/mdwilson/h/intersect-test Best regards, Mike

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Possible bug in dynamic options
by Mutlu Dogruel 28 Aug '12

28 Aug '12

Hi, I wrote a script for dynamically populating a user form. It works but it's slow. When I checked the Galaxy log, I saw that the method called by my custom tool's xml is being run twice (the same debugging lines appear twice in the log, and that happens consistently). Is there any explanation for this? The script returns a list of strings fetched from a remote server. It's running a bit slow, taking up to 6 seconds, so it would be great if I can half that! For testing purposes, I wrote a dummy method that returns a few characters in a list of tuples. Again, my print statement in the Python script is called twice. Has anyone noticed such behaviour? Could it be related to this Galaxy bug: https://bitbucket.org/galaxy/galaxy-central/issue/491/data_column-parameter… The Galaxy script shown on that page says: "NOTE: This is wasteful since dynamic options and dataset collection happens twice (here and when generating HTML)." Thanks. Best regards, -- Mutlu

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Galaxy wiki is throwing errors during edit commit
by Tomithy Too 27 Aug '12

27 Aug '12

Hi Devs, The galaxy wiki is throwing error whenever I try to commit an edit change to it. I have attached a screenshot for your reference. Cheers Tomithy

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Galaxy-France -- Communauté française de Galaxy (French Galaxy Community)
by Dave Clements 27 Aug '12

27 Aug '12

Bonjour à tous, Avec l'aide et le soutien de l'équipe Galaxy, nous venons de mettre en ligne la liste de diffusion Galaxy France. Cette liste a pour but de partager et communiquer sur nos différentes expériences avec Galaxy au sein de l'hexagone. La langue officielle de cette liste est le français. Vous avez besoin d'aide dans l'utilisation de Galaxy, Vous hébergez un serveur public Galaxy, Vous maintenez une instance locale de Galaxy, Vous venez de déposer un outil sur le toolshed, Vous avez des trucs et astuces pouvant interresser la communauté, Vous organisez des formations avec Galaxy, Rejoignez nous en vous inscrivant à http://lists.bx.psu.edu/listinfo/galaxy-france Les archives de cette liste sont disponibles à http://france.list.galaxyproject.org A très bientôt sur la liste Galaxy France, Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer Jackson ------------------------------ --------------------- Hi everyone, With the help and the support of the Galaxy team, we just put online the Galaxy French mailing list. The aim of this list is to share and communicate on our different experiences with Galaxy in France. * The main language is French. * Topics include, but are not limited to: You need help in the use of Galaxy, You're hosting a Galaxy public server, You're maintaining a local instance of Galaxy, You just add a new tool on the toolshed, You have some tips that could interested the community, You organize workshops with Galaxy, Join us by subscribing at http://lists.bx.psu.edu/listinfo/galaxy-france The list's archives are also available at http://france.list.galaxyproject.org See you soon on the Galaxy-France list, The administrators: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer Jackson -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Re: [galaxy-dev] Installing Galaxy and Hooking into a SGE Cluster
by Assaf Gordon 27 Aug '12

27 Aug '12

(Moving to Galaxy-dev, seems more appropriate). John Jones wrote, On 08/23/2012 05:29 PM: > > His original question was about getting Galaxy to recognise LDAP authentication and personal storage space rather than shared storage space as is usual with Galaxy. > Licensing only came into it because Greg wanted LDAP authentication to track individual user usage (for billing) and I questioned the legality of billing for the software used by Galaxy, as I'm sure some components have a non-commercial usage licence clause. > 1. Technically (billing on an SGE cluster): There's a script in "./contrib" called "collect_sge_job_timings.sh" . details are here: http://dev.list.galaxyproject.org/Detailed-SGE-timing-information-about-gal… Assuming you're using PostgreSQL + SGE, it will give you what you want (break-down of SGE jobs timings and Galaxy users). With little adaptation, you can use it to exact SGE JobID and Galaxy Tool-ID / user ID. If you want to extract it directly from the galaxy database, then the following SQL will get you started: === select email as "user", tool_id as "tool", job_runner_external_id as "SGE_ID" from job, galaxy_user where job.user_id = galaxy_user.id and job_runner_name like 'drmaa%' ; === "job_runner_external_ID" will be the SGE-ID, and once you have the list (per each galaxy user), you can use "qacct" to get the information for the job, then calculate the charges. 2. Legally: IANAL, but to the best of my (limited) understanding: 1. Galaxy itself (server code, etc.) - completely legal to run it commercially, even charge money for it - it is licensed as a BSD/MIT style license. 2. Individual tools: if the tools are GPL'd (e.g. bowtie, tophat, bwa, cufflinks) or BSD/MIT - completely legal to run them commercially, and even charge money for them. if the tools use any special license that restrict commercial use (commonly stated as "free for personal, academic, non-commercial use", e.g. Jim Kent's UCSC Genome Browser tools) - then you can't use them in your commercial company without buying a special license (not even internally). It's really not complicated at all, and most (if not all) tools that you compile from source to install them will have a file called "license" or "copying" that will tell you what is the license. If the tools didn't come with a source code, they are probably not free/open-source for commercial use (e.g. - novoalign). 3. Morally: Anyone who thinks of free/open-source as "charity" is missing the point. There is no "charity", and it's perfectly legal, moral, and even recommended to charge money when offering services that are based on free/open-source tools - the requirement (when using GPL) is to give the source code to users when they ask for it (and some other complications, don't want to start a flame war here) - so if they don't want to pay $1,000 for your service - the are more than welcomed to buy their own cluster and storage and servers and run the program themselves - that is the whole point of free/open source. There is not charity. When people write (and publish) software - they explicitly decide upon the license they prefer, and they should know what are the affects of the license. For example, the Galaxy team released Galaxy under a permissive BSD/MIT style license, so they were completely aware of the fact that not only Galaxy can be incorporated into a commercial product, the license doesn't even require the commercial company to release any code changes they make to Galaxy. It's a conscious decision, not an after-thought, and not charity. (end of my rambling...) -gordon

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Tool development without a local Tool Shed?
by Peter Cock 27 Aug '12

27 Aug '12

Dear all, Until recently I'd not needed to define new datatypes while developing tools for Galaxy - instead using (and sometimes modifying) existing datatypes in situ. I have been manually 'installing' my in-development tools by added their XML files to tool_conf.xml - and this has worked fine to date. However, I would now like to experiment with defining or modifying datatypes which would eventually be defined via a datatypes_conf.xml file in a ToolShed entry. My impression from reading the latest wiki documentation on http://wiki.g2.bx.psu.edu/Tool%20Shed is that I will have to install my own local tool shed. Is there a simpler alternative? e.g. Can I add the new datatypes_conf.xml file(s) to a configuration entry instead? Thanks, Peter

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apache external auth and proftpd
by Laure 27 Aug '12

27 Aug '12

Hi galaxy users, I configured galaxy with external ldap authentification using apache proxy, so my galaxy users are automatically created in galaxy database. When I want to configure proftpd to work with galaxy as it is mentionned in galaxy wiki, authentification fails on the ftp because registered password in galaxy_user table mismatchs ldap user password encrypted in SHA1. It seems to be a randomly created password. If I manually translate the ldap password to SHA1, and modify it in galaxy_user table, ftp login works correctly. I wonder how passwords are inserted in galaxy database when users are automatically created ? Is there a way to go through this ? Thanks, Laure

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Declaring dependencies on file format ToolShed entries
by Peter Cock 27 Aug '12

27 Aug '12

Dear all, Is there any way for a Tool Shed bundle (or individual tool) to declare a dependency on another Tool Shed bundle (and ideally a minimum version) which provides a datatype? For example, the 'emboss_5' suite depends on the 'emboss_datatypes' entry. Likewise the ncbi_blast_plus suite depends on 'blast_datatypes' to define the 'blastxml' format (and soon nucleotide and protein BLAST databases). As a specific case, I'd like to update my 'blast2go' wrapper to say it now also depends on blast_datatypes because it uses the 'blastxml' format. Similarly some of my sequence filtering/selection tools could be expanded to handle other formats like 'genbank', which is defined in the 'emboss_datatypes' repository. Regards, Peter

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Changing the location of toolsheddb fails
by Joachim Jacob 27 Aug '12

27 Aug '12

Hi all, I want to change the location of the toolshed database. First I copied all contents to the new location, and next, I adjusted community_wsgi.ini: file_path = /mnt/toolsheddb/community_files However, the toolshed fails to start now, throwing this error: RepoError: repository /home/galaxy/toolshed/database/community_files/000/repo_1 not found It still checks the old location apparently. Thanks for the assistance, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Re: [galaxy-dev] How to speed up job execution
by Hans-Rudolf Hotz 27 Aug '12

27 Aug '12

On 08/24/2012 07:37 PM, kauerbach(a)comcast.net wrote: > Hi Hans, > > I added my email address to the admin_users in universe_wsgi.ini , > logged out of Galaxy, and logged back in but I don't see any 'admin' > tab. Could you tell me what the problem might be? > any change in the "universe_wsgi.ini" file requires a restart of the Galaxy server. Regards, Hans PS: Please keep all replies on the list by using "reply all" in your mail client. > Thank you! > > -Ken. > > ------------------------------------------------------------------------ > > *From: *"Hans-Rudolf Hotz" <hrh(a)fmi.ch> > *To: *kauerbach(a)comcast.net > *Cc: *"Galaxy Development" <galaxy-dev(a)bx.psu.edu> > *Sent: *Friday, August 24, 2012 1:07:20 PM > *Subject: *Re: [galaxy-dev] How to speed up job execution > > > > On 08/24/2012 06:59 PM, kauerbach(a)comcast.net wrote: > > That's very helpful. Thank you. I'm new to Galaxy. Can you tell me how > > to become an 'admin' user and/or change the current admin user? > > > > again, change the settings in "universe_wsgi.ini" by adding your e-mail > (the one you use to log into Galaxy): > > #admin_users = foo(a)bar.com > > > > Regards, Hans > > > > Thank you. > > > > -Ken. > > > > ------------------------------------------------------------------------ > > > > *From: *"Hans-Rudolf Hotz" <hrh(a)fmi.ch> > > *To: *kauerbach(a)comcast.net > > *Cc: *galaxy-dev(a)lists.bx.psu.edu > > *Sent: *Friday, August 24, 2012 12:39:07 PM > > *Subject: *Re: [galaxy-dev] How to speed up job execution > > > > > > > > On 08/24/2012 05:22 PM, kauerbach(a)comcast.net wrote: > > > Hello, > > > > > > On our local instance of Galaxy jobs are taking an extremely long time > > > to run, or they are not run at all. In the history it always says "job > > > is waiting to run", even simple jobs like reformatting text files > to be > > > tab delimited. Is there a way to 1) check the Galaxy job queue, and 2) > > > perhaps modify some parameters to speed up processing? > > > > > > Any suggestions would be greatly appreciated. > > > > > > > Hi Kenneth > > > > Usually, Galaxy is not slow, but the tools executed by Galaxy are slow > > (eg due to bad IO performance of the host server). > > > > "job is waiting to run" indicates there are unfinished jobs in the > > queue. There are two ways to check the queue: > > > > If you are an 'Admin', select the Admin tab -> "Manage jobs". This will > > list all running jobs. And you can kill jobs as well. > > > > Or use the galaxy report tools and have a look at "Today's jobs" > > > > > > > > Depending on your set-up, you might consider changing > "universe_wsgi.ini": > > > > # Number of concurrent jobs to run (local job runner) > > local_job_queue_workers = 5 > > > > to allow more parallel jobs > > > > > > > > Hope this helps > > Hans > > > > > > > > > Thank you. > > > > > > > > > > > > > > > ___________________________________________________________ > > > 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/ > > > > > >

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