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Re: [galaxy-user] [galaxy-dev] Urgent help needed
by Toqa Manasrah 06 Dec '11

06 Dec '11

Thank you so much Dannon. I appreciate your help but I need some more clarification. in the tool I am integrating (which is java classes) if the input parameters are ./main.bash eps0.3_40reads.fa population10_ref.fa 15 6 120 Then teh output is in eps0.3_40reads_I_6_15_CNTGS_DIST0_EM20.txt As u notice the output file name is not specified in teh command line, and actually I dont have the source files to go over this naming restriction. how I can use from_work_dir attribute to tell galaxy this the file to display? note: there are 11 output files and I am interested in this one only ..._CNTGS_DIST0_EM20.txt any other method to overcome such problem I have presentation tomorrwo. hope things will work fine. Thank you, ________________________________________ From: Dannon Baker [dannonbaker(a)me.com] Sent: Monday, December 05, 2011 2:41 PM To: Toqa Manasrah Subject: Re: [galaxy-dev] Urgent help needed Sure. See the link in my previous email (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) and look for the <data> section for an explanation of the attributes available to you. For an example of a tool that uses the from_work_dir element, see the cufflinks, cuff compare, top hat, or trinity wrappers in your galaxy install. -Dannon On Dec 5, 2011, at 2:25 PM, Toqa Manasrah wrote: > Thank you Dannon, > I mean the first choice. no way to specify the output name in tool and it has many putputs but I am intereseted in one only. > > Actually I dont know to use this attribute from_work_dir and I cant find help. can u help plz? > > ________________________________________ > From: Dannon Baker [dannonbaker(a)me.com] > Sent: Monday, December 05, 2011 1:54 PM > To: Toqa Manasrah > Cc: galaxy-dev(a)bx.psu.edu dev; Jennifer Jackson; galaxy-user > Subject: Re: [galaxy-dev] Urgent help needed > > Toqa, > > Just to make sure I've understood your question: the problem is that a tool that you're trying to wrap doesn't provide a way to specify a particular output filename? Take a look at the from_work_dir attribute of a <data> element. > > Or are you asking how to define outputs in general? For that, see the wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E… > > Lastly, for new questions please start new email threads, instead of replying to old ones. This makes it much easier for us to track our responses and make sure people get appropriate help. > > -Dannon > > > On Dec 5, 2011, at 1:26 PM, Toqa Manasrah wrote: > >> Hi Everybody, >> I am running a tool which is not defining the output file name as parameter. >> the tool is running and I can see the output file in the history directory but not in the history frame. >> >> how could I solve the problem? I should see and download the output file from the history but I see an error message instead. the error message not a real error but rather galaxy cannot figure out which file to display? >> >> your help is appreciated, >> >> >> ________________________________________ >> From: Jennifer Jackson [jen(a)bx.psu.edu] >> Sent: Tuesday, November 08, 2011 8:22 AM >> To: Toqa Manasrah >> Cc: Galaxy Dev >> Subject: Re: [galaxy-dev] Installing Galaxy on local server >> >> Hello Tuqa, >> >> Galaxy will not stop by itself. That said, you will want to monitor the >> instance and any associated cluster, just as you would any other >> important processes. >> >> Please send all follow-up with a cc to the mailing list ("reply-all"). >> The development community is a great resource for administrative advice >> and they may have more to add to this reply, i.e. how stable they have >> found Galaxy to be under various conditions. >> >> Best, >> >> Jen >> Galaxy team >> >> On 11/8/11 4:01 AM, Toqa Manasrah wrote: >>> Thank you so much, >>> >>> I did the installation and I ran it under my server. >>> I have one thing concerning about now. if u can help plz. >>> >>> how to run Galaxy in such way that the html interface will continuously working and available for all users visiting the page? >>> >>> i mean how to guarantee that the "sh run.sh" will keep running without any interrupt? >>> >>> Thank you, >>> Tuqa >>> >>> ________________________________________ >>> From: Jennifer Jackson [jen(a)bx.psu.edu] >>> Sent: Thursday, November 03, 2011 6:47 PM >>> To: Toqa Manasrah >>> Cc: galaxy-dev(a)bx.psu.edu >>> Subject: Re: [galaxy-dev] Installing Galaxy on local server >>> >>> Hello Toqa, >>> >>> From your description, this sounds like a local installation for the >>> Galaxy instance itself. Then you can add on a cluster (local or cloud) >>> as needed. >>> >>> Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/ >>> Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed >>> >>> Hopefully the documentation is helpful, >>> >>> Best, >>> >>> Jen >>> Galaxy team >>> >>> On 11/3/11 9:40 AM, Toqa Manasrah wrote: >>>> Hello, >>>> >>>> I am a graduate student at GSU. I am looking for installing GALAXY on >>>> our local server http://alla.cs.gsu.edu/~software. as a result I like my >>>> server homepage start with the GALAXY interface, like this one: >>>> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some >>>> software tolls that we developed in ourdepartment. my primary question >>>> is which option Ihave to choose: Local or cloud? >>>> >>>> looking forward for your help and directions. >>>> >>>> Thank you. >>>> >>>> Tuqa >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> 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/ >>> >>> -- >>> Jennifer Jackson >>> http://usegalaxy.org >>> http://galaxyproject.org/wiki/Support >>> >> >> -- >> Jennifer Jackson >> http://usegalaxy.org >> http://galaxyproject.org/wiki/Support >> >> ___________________________________________________________ >> 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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Re: [galaxy-user] Request to Add Reference Genome
by Jennifer Jackson 06 Dec '11

06 Dec '11

Hello Matt, I am not sure what you mean by an annotated genome, would you be able to send more details? Meanwhile, I can let you know that the tools that use a reference genome (custom or native) all expect a fasta formatted input and use the data directly or create indexes from the data. Any DNA (and sometime RNA) nucleotide fasta file can be used and whether using something other than a complete genome makes sense scientifically is up to the user to determine. Thanks! Jen Galaxy team On 12/5/11 6:59 PM, Matthew Biggs wrote: > Hello Jennifer, > > Thanks for your prompt reply. I had one other question about using a > custom reference genome. Is it possible to use an annotated genome as > the reference for a Bowtie alignment? Using a genome in fasta format is > only so helpful. > > Thanks, > Matt Biggs > > > > > > On Mon, Dec 5, 2011 at 8:24 AM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi Matt, > > The quickest way to use new genomes with most tools, including > Bowtie, is to use them as a custom reference genome. To do this, > load the genome in fasta format into your history. > > Then, on the tool form (for Bowtie, will vary slightly between > tools), set: > > Will you select a reference genome from your history or use a > built-in index?: "Use one from the history" > > The form will refresh, them set: > > Select the reference genome: "dataset_for_your_loaded___genome" > > Best practice: > 1 - double check that the format is strict fasta (all lines > wrapped to same length, no extra lines or hidden characters, > sequence entries are unique within file). > 2 - use the same genome dataset for all steps within an analysis > 3 - load using FTP and make certain load is complete > http://galaxyproject.org/wiki/__Learn/Upload%20via%20FTP > <http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP> > > > Hopefully this helps! > > Best, > > Jen > Galaxy team > > > On 12/3/11 6:37 PM, Matthew Biggs wrote: > > Hello Galaxy Team, > > I am writing to request that the genome of /Sinorhizobium > meliloti /1021 > > be added to the "Map with Bowtie for Illumina" tool. I am using > the main > server http://main.g2.bx.psu.edu/ and my user name is mbiggs. > > Please let me know if this email is received. > > Thanks, > Matt Biggs > > > _____________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org <http://usegalaxy.org>. Please keep all > replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/__listinfo/galaxy-dev > <http://lists.bx.psu.edu/listinfo/galaxy-dev> > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/__Support > <http://galaxyproject.org/wiki/Support> > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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history was empty
by dongdong zhaoweiming 06 Dec '11

06 Dec '11

Hi, I open my galaxy and found the history was empty, I could not found my previous history, so how can I find it? Thanks a lot! Reards weimin zhao

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history was empty
by dongdong zhaoweiming 06 Dec '11

06 Dec '11

Hi, I opened my galaxy and found the history was empty, I could not found my previous history, so how could I find it? Thanks a lot! Reards weimin zhao

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small RNA analysis
by shamsher jagat 05 Dec '11

05 Dec '11

I posted this question previously- IS there any work flow for analysis of microRNA/ small RNA in galaxy, please. I have run microRNA sequencing for control and treated cells. Thanks

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[galaxy-dev] Urgent help needed
by Toqa Manasrah 05 Dec '11

05 Dec '11

Hi Everybody, I am running a tool which is not defining the output file name as parameter. the tool is running and I can see the output file in the history directory but not in the history frame. how could I solve the problem? I should see and download the output file from the history but I see an error message instead. the error message not a real error but rather galaxy cannot figure out which file to display? your help is appreciated, ________________________________________ From: Jennifer Jackson [jen(a)bx.psu.edu] Sent: Tuesday, November 08, 2011 8:22 AM To: Toqa Manasrah Cc: Galaxy Dev Subject: Re: [galaxy-dev] Installing Galaxy on local server Hello Tuqa, Galaxy will not stop by itself. That said, you will want to monitor the instance and any associated cluster, just as you would any other important processes. Please send all follow-up with a cc to the mailing list ("reply-all"). The development community is a great resource for administrative advice and they may have more to add to this reply, i.e. how stable they have found Galaxy to be under various conditions. Best, Jen Galaxy team On 11/8/11 4:01 AM, Toqa Manasrah wrote: > Thank you so much, > > I did the installation and I ran it under my server. > I have one thing concerning about now. if u can help plz. > > how to run Galaxy in such way that the html interface will continuously working and available for all users visiting the page? > > i mean how to guarantee that the "sh run.sh" will keep running without any interrupt? > > Thank you, > Tuqa > > ________________________________________ > From: Jennifer Jackson [jen(a)bx.psu.edu] > Sent: Thursday, November 03, 2011 6:47 PM > To: Toqa Manasrah > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] Installing Galaxy on local server > > Hello Toqa, > > From your description, this sounds like a local installation for the > Galaxy instance itself. Then you can add on a cluster (local or cloud) > as needed. > > Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/ > Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed > > Hopefully the documentation is helpful, > > Best, > > Jen > Galaxy team > > On 11/3/11 9:40 AM, Toqa Manasrah wrote: >> Hello, >> >> I am a graduate student at GSU. I am looking for installing GALAXY on >> our local server http://alla.cs.gsu.edu/~software. as a result I like my >> server homepage start with the GALAXY interface, like this one: >> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some >> software tolls that we developed in ourdepartment. my primary question >> is which option Ihave to choose: Local or cloud? >> >> looking forward for your help and directions. >> >> Thank you. >> >> Tuqa >> >> >> >> ___________________________________________________________ >> 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/ > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/Support > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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bowtie and bwa queue'd up for hours
by Keith Giles 05 Dec '11

05 Dec '11

Does anyone know why these mapping programs are taking so long to start running? Is there a problem with the servers? -- Keith E Giles, PhD Assistant Professor Biochemistry & Molecular Genetics University of Alabama at Birmingham

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upload files
by Bao-Hua Song 05 Dec '11

05 Dec '11

Dear Galaxy experts, I have a question regarding uploading my illumina data (over 3G) using FTP. It was not uploaded completely and stopped. I tried a couple of times..still not working. Can anyone tell me what can cause the problems? Many thanks, Bao

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public interface issues
by Cittaro Davide 05 Dec '11

05 Dec '11

Hi all, I can't use the public interface in an effective way: items in history (i.e. the green boxes) cannot be expanded. More important, names of the items remind me something that has to deal with the tool/library path (e.g. 2010_03/pilot2/README_pilot2_snps). This happens on OS X and MS Windows systems, Firefox and Safari. Thanks d /* Davide Cittaro, PhD Head of Bioinformatics Core Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute Via Olgettina 58 20132 Milano Italy Office: +39 02 26439140 Mail: cittaro.davide(a)hsr.it<mailto:cittaro.davide@hsr.it> Skype: daweonline */

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Re: [galaxy-user] problems loading galaxy histories
by Dave Clements 05 Dec '11

05 Dec '11

Dear Gretel, I am copying this question to the Galaxy-User mailing list, which is the best place to discuss it. Also, see http://galaxyproject.org/wiki/Supportfor other ways to get information. Can you post some additional information to this thread? In particular: * What steps are missing from the histories? Do the steps have anything in common? * Are you trying to view histories that were created on, and have always been stored, on the public Galaxy list; or are you loading a history into that server that was exported from another Galaxy Server? Thanks, Dave C. On Mon, Dec 5, 2011 at 7:26 AM, Gretel Kamm <grtkamm(a)gmx.net> wrote: > Dear Dave Clements, > > I am writing to you because I have been having some problems loading my > user histories at galaxy site. I can log to my count but there are just > some tracks available (the rest of them are not displayed). I don't know > where the problem could be? Perhaps it is the size of the tracks. If that > were the problem, I could delete some of them (if I could see them). I > would appreciate any help you could give me. > > > Regard, > > Gretel Kamm > > > > -- > > Lic. Gretel Kamm > > INGEBI-CONICET > > Vuelta de Obligado 2490 > > 1428 Buenos Aires > > 4783-2871 int. 15 > > Fax 4786-8578 > > e-mail kamm(a)dna.uba.ar > > > NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! > Jetzt informieren: http://www.gmx.net/de/go/freephone > > > -- > > Lic. Gretel Kamm > > INGEBI-CONICET > > Vuelta de Obligado 2490 > > 1428 Buenos Aires > > 4783-2871 int. 15 > > Fax 4786-8578 > > e-mail kamm(a)dna.uba.ar > > > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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