galaxy-user

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3031 discussions

Galaxy-User has moved to Galaxy Biostar
by Dave Clements 07 Jun '14

07 Jun '14

Hello all, After 8+ years and more than 8100 posts, the Galaxy-User mailing list has been retired. But, don't worry, you can still get Galaxy user support at Galaxy Biostar (https://biostar.usegalaxy.org/), an online user support forum that has replaced this list. Past postings to this list are available at Galaxy Biostar. All existing archives of this list will also remain available. See the Galaxy Support page (https://wiki.galaxyproject.org/Support) and the Galaxy Mailing List page (https://wiki.galaxyproject.org/MailingLists) for all support options. Thanks for making Galaxy-User, and Galaxy Biostar, such great resources. See you online, Dave C and the Galaxy Team -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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CummeRbund on Galaxy
by Ganote, Carrie L 03 Jun '14

03 Jun '14

Hi list, Is the cummeRbund wrapper on Galaxy yet functional? I've got some replicates that I'm trying to test for a user on our local Galaxy, but I just can't get the program to behave. Using cuffdiff v2.2.0 604fa75232a2 cummeRbund version 0.0.7, 137aab1d9ac1 R 2.15.2 and 3.0.1 (tried both) Last galaxy-dist/stable changeset: 7a7985a007fb I ran cuffdiff like so: Transcripts 83: Cuffmerge on data 6, data 67, and others: merged transcripts Name control Add replicate 44: Tophat2 on data 1 and data 6: accepted_hits (ran as single-end fastq) Add replicate 54: Tophat2 on data 2 and data 6: accepted_hits (ran as single-end fastq) Name sample Add replicate 59: Tophat2 on data 3 and data 6: accepted_hits (ran as single-end fastq) Add replicate 64: Tophat2 on data 4 and data 6: accepted_hits (ran as single-end fastq) Library normalization method geometric Dispersion estimation method pooled False Discovery Rate 0.05 Min Alignment Count 10 Use multi-read correct No Perform Bias Correction No Include Read Group Datasets No Set Additional Parameters? (not recommended for paired-end reads) No Here's what I get when I run cummeRbund: (From Galaxy, with R 2.15.2) Creating database //path/job_working_directory/005/5051/galaxy_dataset_16602.dat Reading //path/dataset_files/009/dataset_9861.dat Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading //path/dataset_files/009/dataset_9861.dat Error in function (classes, fdef, mtable) : unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"' Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous> Execution halted (From R interpreter on command line, R = 3.0.1) Reading //path/dataset_files/009/dataset_9842.dat Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading //path/dataset_files/009/dataset_9842.dat Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"' In addition: Warning message: attributes are not identical across measure variables; they will be dropped I tried changing the group names in cuffdiff but no luck. No spaces or funny characters. Thanks for any insight, Carrie Ganote

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June 2, 2014 Galaxy Distribution
by Jennifer Jackson 02 Jun '14

02 Jun '14

June 2, 2014 Galaxy Distribution <http://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution> *News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2014_06_02>**Highlights:* * Dataset Collections introduced * Changes to database build (dbkey) organization * Enhancements to Tool configuration and Workflow options * Trackster, User Interface, and Admin panel upgrades * Significant updates to Admin and Job functionality * Tool Shed repository and API additions * Data updates plus new Security features and Bug fixes * new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2014.06.02 getgalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy> galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/> bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* * /Thanks for using Galaxy!/ The Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam>

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(no subject)
by Ianiri, Giuseppe 02 Jun '14

02 Jun '14

Hi, I uploaded some file that resulted to be too big and my history showed that that was not more space available. Now I deleted few file, and I should have 80 GB available, but my history shows still that I have no more space available for analysis. Can anyone from the Galaxy team check this for me? Giuseppe

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Galaxy User List Being Retired on June 6, 2014.
by Dave Clements 02 Jun '14

02 Jun '14

Hello all, In case you didn't see this it the June Galaxy Newsletter <http://bit.ly/SX3MuS> that went out today: Galaxy-User Being Retired June 6 [image: Galaxy Biostar] <https://biostar.usegalaxy.org/> Join the conversation! Learn how here <https://wiki.galaxyproject.org/Support/Biostar>. The *Galaxy Biostar <https://biostar.usegalaxy.org/>* online forum was launched April 23 as a replacement for the Galaxy-User mailing list <https://wiki.galaxyproject.org/MailingLists>. During the past 5 weeks, Galaxy Biostar has been wildly successful with over 125 active threads, *more than 5 times the number of active threads on Galaxy-user in the 5 weeks before the switch.* Galaxy-User has remained open during the transition, but now it's time to retire it. All new posting to Galaxy-User will be stopped on Friday, June 6, *some 101 months, and 8,100 postings* after it was launched. All those postings will remain available both in Galaxy Biostar (where they have been imported), and in the online list archives <http://user.list.galaxyproject.org/>. Thanks for making Galaxy Biostar, and Galaxy-User before it, such a great resource. Thanks again, Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Re: [galaxy-user] galaxy-user Digest, Vol 95, Issue 9
by Les Dethlefsen 27 May '14

27 May '14

Actually, if the ones I ordered last year are expiring soon, I'd suggest people continue to use those before recently ordered kits. Les ----- Original Message ----- > Send galaxy-user mailing list submissions to > galaxy-user(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to > the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread you > are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from > the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search > queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: Urgent Question about PostgreSQL Compatibility > (Paniagua, Eric) > 2. Re: Urgent Question about PostgreSQL Compatibility (Dannon Baker) > 3. Re: Urgent Question about PostgreSQL Compatibility > (Paniagua, Eric) > 4. Re: Urgent Question about PostgreSQL Compatibility > (Paniagua, Eric) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 23 May 2014 19:49:02 +0000 > From: "Paniagua, Eric" <epaniagu(a)cshl.edu> > To: Dannon Baker <dannon.baker(a)gmail.com> > Cc: Galaxy ?[galaxy-user(a)bx.psu.edu]? <galaxy-user(a)bx.psu.edu> > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL > Compatibility > Message-ID: > <759E5BE3A1277B48ADEE4096E39269CBB22248AD(a)EX-HS-MBX05.cshl.edu> > Content-Type: text/plain; charset="windows-1256" > > Hi Dannon, > > There have been some developments, and I would like to update my question > accordingly. > > I have set up PostgreSQL 9.1 on a separate box from our Galaxy server, and > ferried the database contents over. My question is this: > > What is the appropriate syntax to use for the parameter "database_connection" > in universe_wsgi.ini to use a remote database server? Specifically: > > Galaxy host: genomics.cshl.edu > Database host: wigserv5.cshl.edu > Database name: glxeric > Database user/role: glxeric > Database port: 5432 (postgresql default port) > Database password: not required under the current configuration. > > Can someone please explain how to fill in the "database_connection" parameter > appropriately? > > Many thanks, > Eric > > ________________________________________ > From: galaxy-user-bounces(a)lists.bx.psu.edu > [galaxy-user-bounces(a)lists.bx.psu.edu] on behalf of Paniagua, Eric > [epaniagu(a)cshl.edu] > Sent: Thursday, May 22, 2014 1:38 PM > To: Dannon Baker > Cc: Galaxy ?[galaxy-user(a)bx.psu.edu]? > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility > > Hi Dannon, > > I have attached a screenshot of the error as it appears in the Galaxy web > site and a screenshot of the log. > > Please let me know if I can provide any more information. > > Also, please note that the version information I gave for PostgreSQL before > was incorrect. I am actually running PostgreSQL 8.1.22. > > Thanks for your assistance, > Eric > > ________________________________________ > From: galaxy-user-bounces(a)lists.bx.psu.edu > [galaxy-user-bounces(a)lists.bx.psu.edu] on behalf of Paniagua, Eric > [epaniagu(a)cshl.edu] > Sent: Thursday, May 22, 2014 11:14 AM > To: Dannon Baker > Cc: Galaxy ?[galaxy-user(a)bx.psu.edu]? > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility > > Hi Dannon, > > I am in a meeting right now. I should be done at noon. I'll send you more > info then. Thank you for your assistance! > > Best, > Eric > > > -------- Original message -------- > From: Dannon Baker > Date:2014/05/22 11:08 (GMT-05:00) > To: "Paniagua, Eric" > Cc: "Galaxy ?[galaxy-user(a)bx.psu.edu]?" > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility > > Hey Eric, > > Looking into this. Can you send the exact error/trace if available? > > -Dannon > > > On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric > <epaniagu(a)cshl.edu<mailto:epaniagu@cshl.edu>> wrote: > Hi, > > I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in the > process of preparing an update I have encountered some problems. When I try > to create a new dataset (e.g. by running a tool), I receive an error message > indicating a syntactic problem with backend database commands. > Specifically, the error mentions a read-only cursor and occurs when the > system is trying to look up the history hid number for the new dataset, a > value which (as far as I understand it) should be an autoincrementing > primary key. > > My codebase is the 68a8b0397947 commit on the stable branch, plus some custom > tool definitions, but no real modification to any core Galaxy code. The > database I am using is PostgreSQL 9.1. I am using Python 2.6.4. In the > target (production) environment, we run with 3 web server processes and 3 > job runner processes, but I am encountering this error in a > single-Galaxy-process test instance. The error is reported both in the logs > (with a traceback originating in the bowels of SQLAlchemy) and via the web > interface. > > I dug through the commit history and found a comit (e1bc855165bc) with the > comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4)." > on Sep 23, 2013. I am wondering if this means I need to upgrade my database > backend to PostgreSQL 2.4.x. The wrinkle lies in the fact that I need to > keep 2 parallel Galaxy instances running for an extended time period (~1 > month). The first is the current (not updated) local Galaxy instance, and > the second is the new (updated) Galaxy instance, which naturally implies > diverging databases. Does this mean I will need to maintain parallel > installations of PostgreSQL 9.1 and 9.2.x? How would I go about setting up > that configuration? > > Any assistance on debugging this error would be greatly appreciated. Our > initial goal was to roll out this update tomorrow afternoon, but that may > need to be delayed because of this show-stopper. If I can provide any > further useful information, please let me know, and I will be happy to do > so. > > Best, > Eric Paniagua > > ___________________________________________________________ > The Galaxy User List is being replaced by the Galaxy Biostar > User Support Forum at https://biostar.usegalaxy.org/ > > Posts to this list will be disabled in May 2014. In the > meantime, you are encouraged to post all new questions to > Galaxy Biostar. > > 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 > > 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/ > > > ___________________________________________________________ > The Galaxy User List is being replaced by the Galaxy Biostar > User Support Forum at https://biostar.usegalaxy.org/ > > Posts to this list will be disabled in May 2014. In the > meantime, you are encouraged to post all new questions to > Galaxy Biostar. > > 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 > > 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/ > > > > ------------------------------ > > Message: 2 > Date: Fri, 23 May 2014 16:02:41 -0400 > From: Dannon Baker <dannon.baker(a)gmail.com> > To: "Paniagua, Eric" <epaniagu(a)cshl.edu> > Cc: Galaxy ?[galaxy-user(a)bx.psu.edu]? <galaxy-user(a)bx.psu.edu> > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL > Compatibility > Message-ID: > <CAGn_WZnY9BV9HAsMSekCDdrqUbtSGjTieRG=s75_oHxewnHrXQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hey Eric, > > We use sqlalchemy, and the detailed documentation is here: > > http://docs.sqlalchemy.org/en/rel_0_7/core/engines.html#postgresql > > That said, the basic format is: dialect+driver://username:password@host > :port/database > > So, you're going to be looking at something like: postgres:// > glxeric@wigserv5.cshl.edu:5432/glxeric > > > > On Fri, May 23, 2014 at 3:49 PM, Paniagua, Eric <epaniagu(a)cshl.edu> wrote: > > > Hi Dannon, > > > > There have been some developments, and I would like to update my question > > accordingly. > > > > I have set up PostgreSQL 9.1 on a separate box from our Galaxy server, and > > ferried the database contents over. My question is this: > > > > What is the appropriate syntax to use for the parameter > > "database_connection" in universe_wsgi.ini to use a remote database server? > > Specifically: > > > > Galaxy host: genomics.cshl.edu > > Database host: wigserv5.cshl.edu > > Database name: glxeric > > Database user/role: glxeric > > Database port: 5432 (postgresql default port) > > Database password: not required under the current configuration. > > > > Can someone please explain how to fill in the "database_connection" > > parameter appropriately? > > > > Many thanks, > > Eric > > > > ________________________________________ > > From: galaxy-user-bounces(a)lists.bx.psu.edu [ > > galaxy-user-bounces(a)lists.bx.psu.edu] on behalf of Paniagua, Eric [ > > epaniagu(a)cshl.edu] > > Sent: Thursday, May 22, 2014 1:38 PM > > To: Dannon Baker > > Cc: Galaxy ?[galaxy-user(a)bx.psu.edu]? > > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility > > > > Hi Dannon, > > > > I have attached a screenshot of the error as it appears in the Galaxy web > > site and a screenshot of the log. > > > > Please let me know if I can provide any more information. > > > > Also, please note that the version information I gave for PostgreSQL > > before was incorrect. I am actually running PostgreSQL 8.1.22. > > > > Thanks for your assistance, > > Eric > > > > ________________________________________ > > From: galaxy-user-bounces(a)lists.bx.psu.edu [ > > galaxy-user-bounces(a)lists.bx.psu.edu] on behalf of Paniagua, Eric [ > > epaniagu(a)cshl.edu] > > Sent: Thursday, May 22, 2014 11:14 AM > > To: Dannon Baker > > Cc: Galaxy ?[galaxy-user(a)bx.psu.edu]? > > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility > > > > Hi Dannon, > > > > I am in a meeting right now. I should be done at noon. I'll send you > > more info then. Thank you for your assistance! > > > > Best, > > Eric > > > > > > -------- Original message -------- > > From: Dannon Baker > > Date:2014/05/22 11:08 (GMT-05:00) > > To: "Paniagua, Eric" > > Cc: "Galaxy ?[galaxy-user(a)bx.psu.edu]?" > > Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility > > > > Hey Eric, > > > > Looking into this. Can you send the exact error/trace if available? > > > > -Dannon > > > > > > On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric <epaniagu(a)cshl.edu > > <mailto:epaniagu@cshl.edu>> wrote: > > Hi, > > > > I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in > > the process of preparing an update I have encountered some problems. When > > I try to create a new dataset (e.g. by running a tool), I receive an error > > message indicating a syntactic problem with backend database commands. > > Specifically, the error mentions a read-only cursor and occurs when the > > system is trying to look up the history hid number for the new dataset, a > > value which (as far as I understand it) should be an autoincrementing > > primary key. > > > > My codebase is the 68a8b0397947 commit on the stable branch, plus some > > custom tool definitions, but no real modification to any core Galaxy code. > > The database I am using is PostgreSQL 9.1. I am using Python 2.6.4. In > > the target (production) environment, we run with 3 web server processes and > > 3 job runner processes, but I am encountering this error in a > > single-Galaxy-process test instance. The error is reported both in the > > logs (with a traceback originating in the bowels of SQLAlchemy) and via the > > web interface. > > > > I dug through the commit history and found a comit (e1bc855165bc) with the > > comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL > > 9.2.4)." on Sep 23, 2013. I am wondering if this means I need to upgrade > > my database backend to PostgreSQL 2.4.x. The wrinkle lies in the fact that > > I need to keep 2 parallel Galaxy instances running for an extended time > > period (~1 month). The first is the current (not updated) local Galaxy > > instance, and the second is the new (updated) Galaxy instance, which > > naturally implies diverging databases. Does this mean I will need to > > maintain parallel installations of PostgreSQL 9.1 and 9.2.x? How would I > > go about setting up that configuration? > > > > Any assistance on debugging this error would be greatly appreciated. Our > > initial goal was to roll out this update tomorrow afternoon, but that may > > need to be delayed because of this show-stopper. If I can provide any > > further useful information, please let me know, and I will be happy to do > > so. > > > > Best, > > Eric Paniagua > > > > ___________________________________________________________ > > The Galaxy User List is being replaced by the Galaxy Biostar > > User Support Forum at https://biostar.usegalaxy.org/ > > > > Posts to this list will be disabled in May 2014. In the > > meantime, you are encouraged to post all new questions to > > Galaxy Biostar. > > > > 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 > > > > 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/ > > > > > > ___________________________________________________________ > > The Galaxy User List is being replaced by the Galaxy Biostar > > User Support Forum at https://biostar.usegalaxy.org/ > > > > Posts to this list will be disabled in May 2014. In the > > meantime, you are encouraged to post all new questions to > > Galaxy Biostar. > > > > 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 > > > > 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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slow running
by Emmanuelle Lerat 27 May '14

27 May '14

Hi everyone, I am currently running a fastqgroomer on some data (about 7Go big). I am surprise because I launched the analysis several hours ago and it is still running. I am wondering if everything is alright since usually it is faster than that, even on bigger dataset. I had the same problem yesterday with fastQC that was not finished after 24h also it was indicated as running (I finally discarded this job) Is the galaxy sever busy or do you think it is because of my data? thank you in advance for your help Sincerely Emmanuelle Lerat -- Dr. Emmanuelle LERAT, CR1 CNRS, HDR Laboratoire Biometrie et Biologie Evolutive Universite Claude Bernard - Lyon 1 UMR-CNRS 5558 - Bat. Mendel 43 bd du 11 novembre 1918 69622 Villeurbanne cedex France Phone: 33+ 4.72.43.29.18 Fax: 33+ 4.72.43.13.88 http://lbbe.univ-lyon1.fr/-Lerat-Emmanuelle-.html

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Re: [galaxy-user] Asking for help from China about Galaxy Project
by Enis Afgan 24 May '14

24 May '14

You can upload the required genome into your history and then from the "Use a built in reference genome or own from your history:" dropdown choose "use a genome from history" option of the Tophat tool. Tophat will then run using the desired reference genome. BTW, these types of questions are best asked on the Biostar Q&A site for Galaxy (https://biostar.usegalaxy.org/) or the user mailing list (CC'd). That will give you better exposure to the community and hence a better chance for an answer. Hope this help, Enis On Sat, May 24, 2014 at 9:43 AM, shiny <shishishiny(a)foxmail.com> wrote: > Hello,Enis Afgan. > I wonna run TOPHAT through the Galaxy project.Well, I can't find the > reference genome of *Carica papaya.*So should I ask for help as it shows > on the website,or it is easier should I turn to use Linux shell for me? > Shiny >

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Urgent Question about PostgreSQL Compatibility
by Paniagua, Eric 23 May '14

23 May '14

Hi, I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in the process of preparing an update I have encountered some problems. When I try to create a new dataset (e.g. by running a tool), I receive an error message indicating a syntactic problem with backend database commands. Specifically, the error mentions a read-only cursor and occurs when the system is trying to look up the history hid number for the new dataset, a value which (as far as I understand it) should be an autoincrementing primary key. My codebase is the 68a8b0397947 commit on the stable branch, plus some custom tool definitions, but no real modification to any core Galaxy code. The database I am using is PostgreSQL 9.1. I am using Python 2.6.4. In the target (production) environment, we run with 3 web server processes and 3 job runner processes, but I am encountering this error in a single-Galaxy-process test instance. The error is reported both in the logs (with a traceback originating in the bowels of SQLAlchemy) and via the web interface. I dug through the commit history and found a comit (e1bc855165bc) with the comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4)." on Sep 23, 2013. I am wondering if this means I need to upgrade my database backend to PostgreSQL 2.4.x. The wrinkle lies in the fact that I need to keep 2 parallel Galaxy instances running for an extended time period (~1 month). The first is the current (not updated) local Galaxy instance, and the second is the new (updated) Galaxy instance, which naturally implies diverging databases. Does this mean I will need to maintain parallel installations of PostgreSQL 9.1 and 9.2.x? How would I go about setting up that configuration? Any assistance on debugging this error would be greatly appreciated. Our initial goal was to roll out this update tomorrow afternoon, but that may need to be delayed because of this show-stopper. If I can provide any further useful information, please let me know, and I will be happy to do so. Best, Eric Paniagua

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Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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