galaxy-proteomics

galaxy-proteomics@lists.galaxyproject.org

20 discussions

TOPPview in Galaxy
by Martin Hubálek 27 Nov '17

27 Nov '17

Hi, I would like to get an advice on using OpenMS in Galaxy, especially on connecting TOPPview to visualize the results. Can anyone help me? Thanks, Martin -- Martin Hubálek, Ph.D. Institute of Organic Chemistry and Biochemistry, CAS Flemingovo nám. 2, 16610 Praha 6, Czech Republic tel.: 220183117

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Fwd: [galaxy-dev] Galaxy Proteomics Hackathon
by Dave Clements 09 Sep '16

09 Sep '16

>From Pratik & Björn: Hi all! I would like to spread the news from the GalaxyP team about a new hackthon. Please join and help us if you have some time! ********************* The first Galaxy-P CONDA hackathon will be held on September 27th and 28th. Galaxy-P and proteomics tool developers will participate in this hackathon to "CONDA-package" some of the prioritized proteomics tools within Galaxy. The hackathon will be an online event which will start with an introduction to Galaxy structure and CONDA packaging by Bjoern Gruening. https://github.com/galaxyproteomics/tools-galaxyp/issues/57 Details soon. Please see if you would like to publicize this. Thanks and Regards, Pratik ___________________________________________________________ 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/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Galaxy at 64th ASMS Conference on Mass Spectrometry and Allied Topics
by Dave Clements 16 May '16

16 May '16

Hello all, And while I'm at it, I should have posted this a month ago: Galaxy will again have a strong presence <https://wiki.galaxyproject.org/Events/ASMS2016> at ASMS, including talks, posters, and a workshop <https://wiki.galaxyproject.org/Events/ASMS2016#Workshop_14:_Galaxy_for_Prot…> . Check it out. Cheers, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Proteomics Galaxy Servers
by Dave Clements 16 May '16

16 May '16

Hi All, I always mean to do this when I add servers to the Public Galaxy Servers list (https://wiki.galaxyproject.org/PublicGalaxyServers), and I almost always forget. So, here it is all in one bundle (until the next time I remember). In case you are interested the Public Galaxy Server list lists n servers that are about proteomics: - ballaxy <https://wiki.galaxyproject.org/PublicGalaxyServers#ballaxy> - CAPER <https://wiki.galaxyproject.org/PublicGalaxyServers#CAPER> - GIO <https://wiki.galaxyproject.org/PublicGalaxyServers#Galaxy_Integrated_Omics_…> - Galaxy-P <https://wiki.galaxyproject.org/PublicGalaxyServers#Galaxy-P> - Halogen Bonding <https://wiki.galaxyproject.org/PublicGalaxyServers#Halogen_Bonding> - SymD <https://wiki.galaxyproject.org/PublicGalaxyServers#SymD> and several more <https://wiki.galaxyproject.org/PublicGalaxyServers?highlight=%28protein%29%…> that have proteomic tools. If you know of any other sites please let me know. And, if you see something that particularly grabs you I recommend contacting the site owners and/or using the site. And, don't forget to register for GCC2016, and submit your posters and demos *this week <https://gcc2016.iu.edu/registration/index.php>*. Cheers, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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toolshed
by Jorrit Boekel 07 Apr '16

07 Apr '16

Hi Galaxy-P, I would like to package some tools for the toolshed and include them in the Galaxy-P github repo. The tools are: - percolator and pout2mzid - hardklor/kronik - msstitch (aka my own tool) And maybe some isobaric protein quant R script, and/or updates to MSGF+. Anyway, I have poked around a little and have no problems creating and testing tools. However the toolshed syntax is a bit confusing. I understand I have to specify a package definition (tool_dependencies.xml) which installs the tool. And then the tool itself, which seems easy enough. My questions about this: - Is there any doc on the toolshed XML that defines how you install your binaries? I am planning to build from source, since percolator has binaries for different linuxes. (If it is not possible to specify which one of those to use.) - what is in the admin-scripts directory? Static data? Hoping to submit pull requests soon! cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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sqlite datatype
by Jorrit Boekel 13 Feb '15

13 Feb '15

Hi JJ and mailing list, I think it was John who mailed earlier about implementing an SQLite datatype for proteomics. I sort of like this, since I find myself using SQLite all the time for my own command line tool to do filtering, protein grouping, and relating quant output to ID data. https://github.com/glormph/msstitch — I basically wrote this to combine percolator, mzidentml, and openMS intermediate formats. It’s currently a bit of a mixture of different databases and tables for different operations, but maybe it would be a good idea to have one large proteomics experiment SQLite database. Note that this is nothing I want to push onto people like it would be the next PSI standard, more like a very convenient and fast intermediate datatype. I believe that the proteome discoverer msf files are also based on sqlite. While I’m not sure if it’s a good fit for a server environment since it can get locking/access problems when accessed by too many processes, it’s a very nice fit for a bioinformatic cli tool. Are you guys currently working on any standardized SQLite thing? cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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galaxy community conference
by Jorrit Boekel 13 Feb '15

13 Feb '15

Hi all, Before I start planning my attendance, are Galaxy proteomics people going to be at the GCC in Norwich? cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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Mailing list moved, but not to Google Groups
by Dave Clements 22 Nov '14

22 Nov '14

Hello all, This mailing list has a new home! But it isn't Google Groups. Yesterday Nate moved this list from the lists.bx.psu.edu domain to the lists.galaxyproject.org domain. This gives us better control over the list, including spam. This transition should be largely transparent to you, but there are a few things to be aware of: - List sender addresses and headers will change to reflect the updated domain: from bx.psu.edu togalaxyproject.org. Existing email filters you have set up may require adjustments. - Posts from lists.galaxyproject.org could be categorized as spam until you train your filtering method. - Mailing list archives and posting functionality will be briefly inaccessible during the migration. - The prior bx.psu.edu list posting email addresses will continue to accept email, which will be forwarded to the new list addresses. What happened to the Google Groups plan, you might ask. Well, we used Google Groups for the GCC2014 mailing lists and they were problematic. It turns out that many people's work email servers periodically identify Google Groups as a spammer and then just block it causing emails from the list to silently stop being delivered. Not exactly the behavior you want in a mailing list. Please let us know if you have any questions. Thanks, Dave C and Nate On Thu, May 22, 2014 at 12:17 PM, Dave Clements <clements(a)galaxyproject.org> wrote: > Hello Galaxy Proteomicists! > > The Galaxy Project has started to create new mailing lists using a Google > Groups infrastructure. The new lists still work like mailing lists (plus > other stuff). We are hoping that Google Groups proves to be less > maintenance than Mailman. We are also considering moving our established > lists to Google too. > > Since this is the smallest and least active of the Galaxy community's > mailing lists, this is the first established list we are going to move. > Look for this to happen before GCC2014. > > If anyone has any requests or questions about the move, please let us know. > > Thanks, > > Dave C > > PS: John Chilton originally wanted this list set up on Google Groups. I > talked him out of it. There can't possibly be a lesson for me in that > experience, can there? ;-) > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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question about configuring MaxQuant and LWR on Galaxy
by Mateus Bellomo 30 Jun '14

30 Jun '14

Hi everyone, I'am trying to configure Galaxy to run MaxQuant but I'm having a little trouble. I already installed LWR and checked that it's running ok (it's running by command line and call for MaxQuant). I also confirmed that Galaxy is listenning to LWR. I've installed the package of datatypes provided by iracooke so I can upload the raw files do Galaxy. To configure the LWR I've copied some files of Galaxy-p. When I try to submit a job to the MaxQuant tool on Galaxy I get an error that I can see on the Windows terminal that is running the LWR. The error is: AttributeError : "InputsValidator" object has no attribute 'validate_configfile' I've noticed that this occurs in a python script of LWR tool. I've searched for this bug for hours without success. Any help would be appreciated. Thanks in advance

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Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy Workshop?
by Ira Cooke 30 May '14

30 May '14

Many thanks Dave and Pratik, This list is a great resource. On 31 May 2014, at 6:47 am, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> wrote: Hi All, Many thanks to Pratik for sending on several new talks and posters, and details about the workshop: https://wiki.galaxyproject.org/Events/ASMS2014 or http://bit.ly/asms2014 Please let me know if there is anything else. Thanks, Dave C On Fri, May 30, 2014 at 9:17 AM, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> wrote: Hello all, If you are going to ASMS, all things Galaxy (I found 5) are listed at: https://wiki.galaxyproject.org/Events/ASMS2014 or http://bit.ly/asms2014 It prints out nicely. Feel free to take a few copies with you. Thanks, Dave C. On Thu, May 29, 2014 at 4:34 PM, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> wrote: Hi Pratik, John, and Jorrit, Thanks for all the suggestions and input. The good news is that I can wait for a new Galaxy-P 101 to be released. Perhaps fearing my complete lack of knowledge in proteomics, the workshop hosts have opted to have me cover topics that I can at least spell instead. However, long-term, it would be a wonderful thing to have a Galaxy proteomics worked example that people could use in workshops. And Jorrit, I just looked at the program for ASMS. There are several Galaxy related workshops, talks and posters this year. I'll create a wiki page listing everything, and perhaps a flyer ... I'll post to this list once that's ready. Thanks for everything, Dave C. On Thu, May 29, 2014 at 12:11 AM, Jorrit Boekel <jorrit.boekel(a)scilifelab.se<mailto:jorrit.boekel@scilifelab.se>> wrote: Hey Dave, An alternative to the problem John mentions would be to skip the RAW files altogether and start from a mzML data file downloaded from a repository (e.g. proteomexhange.org<http://proteomexhange.org/>) somewhere. To abstract your workshop from the fact that mass spec instrument manufacturers don’t provide proper accessible output formats. Hope to see many of you at ASMS in two weeks! cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 29 May 2014, at 00:20, John Chilton <jmchilton(a)gmail.com<mailto:jmchilton@gmail.com>> wrote: > Hey Dave, > > Yeah the example is pretty old and it seems the Galaxy-P team no > longer distributes a Galaxy-P specific code base - but *in theory* one > should be able to get most of the needed tools from the tool shed. If > you attempt this tutorial on a fresh instance of Galaxy you are not > going to be able to do the very first step though - extracting raw > files. This requires a Windows server for Galaxy to communicate with > the LWR or a customized WINE emulation environment. Perhaps you can do > the first step on the public Galaxy-P server and just take the > resulting file and do your analysis from there on? Good luck :). > > -John > > > On Sat, May 24, 2014 at 7:33 AM, Pratik Jagtap <pjagtap(a)umn.edu<mailto:pjagtap@umn.edu>> wrote: >> Hello Dave, >> >> Thanks for the mail. >> >> The Galaxy-P 101 was written and used by us (John Chilton and myself) in >> November 2012 and it was last tested in July 2013. It will be great if >> anyone has an opportunity to see if and how it works. >> >> There is a need for a new GalaxyP 101 - which we will do so after we have >> new set of tools such as MS-GF+ and PeptideShaker installed. As we publish, >> we will also have pages and tutorials for proteogenomics and metaproteomics >> workflows. >> >>> Galaxy-P folks: How do you feel about others using the Galaxy-P 101 in > >>> workshops? I can imagine installing all the tools on the workshop servers > >>> (in which case it seems like an easy win), or running directly off Galaxy-P >>> (which would better highlight Galaxy-P, but put a load on your servers). >> >> Once tested, I think it is a good idea to have GalaxyP101 on the workshop >> servers. >> >> For most of our proteomics work - we have been using ProteinPilot ( a >> Windows-based commercial tool). We have a webinar available in case users >> are interested - z.umn.edu/ppingp<http://z.umn.edu/ppingp> >> >> Thanks and Regards, >> >> Pratik >> >> Pratik Jagtap, >> Managing Director, >> Center for Mass Spectrometry and Proteomics, >> 43 Gortner Laboratory >> 1479 Gortner Avenue >> St. Paul, MN 55108 >> Phone: 612-624-9275 >> >> >> On Fri, May 23, 2014 at 11:54 AM, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> >> wrote: >>> >>> Hi Pratik and JJ, >>> >>> Just a heads up that there's a relevant thread on the Galaxy-Proteomics >>> list that you might want to respond to. >>> >>> Bart is on the list, but I don't think either of you are. If you respond, >>> please respond on-list, if you are comfortable with that. >>> >>> Thanks, >>> >>> Dave C >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> >>> Date: Fri, May 23, 2014 at 9:52 AM >>> Subject: Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy >>> Workshop? >>> To: Ira Cooke <I.Cooke(a)latrobe.edu.au<mailto:I.Cooke@latrobe.edu.au>> >>> Cc: Galaxy Proteomics List <galaxy-proteomics(a)lists.bx.psu.edu<mailto:galaxy-proteomics@lists.bx.psu.edu>> >>> >>> >>> Hi Ira, >>> >>> Thanks for the pointer. And many thanks to the Galaxy-P folks for >>> creating this. In hindsight (which I'm really good at), Galaxy-P seems an >>> obvious place to look for this. >>> >>> The example looks enormous, but it's well documented. I'll give it a >>> careful look. >>> >>> And, for this workshop and for future reference: >>> >>> Galaxy-P folks: How do you feel about others using the Galaxy-P 101 in >>> workshops? I can imagine installing all the tools on the workshop servers >>> (in which case it seems like an easy win), or running directly off Galaxy-P >>> (which would better highlight Galaxy-P, but put a load on your servers). >>> >>> Thanks again, >>> >>> Dave C. >>> >>> >>> >>> >>> On Thu, May 22, 2014 at 5:36 PM, Ira Cooke <I.Cooke(a)latrobe.edu.au<mailto:I.Cooke@latrobe.edu.au>> wrote: >>>> >>>> Hi Dave, >>>> >>>> I haven’t gone through it myself, but this looks good >>>> >>>> https://usegalaxyp.readthedocs.org/en/latest/sections/galaxyp_101.html >>>> >>>> Cheers >>>> Ira >>>> >>>> >>>> On 23 May 2014, at 5:11 am, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> >>>> wrote: >>>> >>>> Hello all, >>>> >>>> Does anyone know of worked proteomics analysis that I could use for a >>>> Galaxy workshop? I'm giving a workshop in July and the hosts are interested >>>> in proteomics. I did tell them I currently have no knowledge of proteomics, >>>> so they aren't expecting me to cover it. However, if a ready made example >>>> is out there, I might be able to come up to speed on the basics before then >>>> >>>> Thanks, >>>> >>>> Dave C >>>> >>>> -- >>>> http://galaxyproject.org/GCC2014 >>>> http://galaxyproject.org/ >>>> http://getgalaxy.org/ >>>> http://usegalaxy.org/ >>>> https://wiki.galaxyproject.org/ >>>> _______________________________________________ >>>> 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/ >>>> >>>> >>> >>> >>> >>> -- >>> http://galaxyproject.org/GCC2014 >>> http://galaxyproject.org/ >>> http://getgalaxy.org/ >>> http://usegalaxy.org/ >>> https://wiki.galaxyproject.org/ >>> >>> >>> >>> -- >>> http://galaxyproject.org/GCC2014 >>> http://galaxyproject.org/ >>> http://getgalaxy.org/ >>> http://usegalaxy.org/ >>> https://wiki.galaxyproject.org/ >> >> >> >> _______________________________________________ >> 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/ -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ _______________________________________________ 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/

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