galaxy-user May 2014

galaxy-user@lists.galaxyproject.org

16 participants
13 discussions

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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please delete me from the mailing list!!!!
by Anna J. 21 May '14

21 May '14

please delete me from the mailing list!!!!

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Cuffmerge not working with reference genome
by Mark Lindsay 20 May '14

20 May '14

Dear All when I run Cuffmerge using the latest GenCode v19 GTF as a reference genome….this fails to run…tried this using multiple approaches and datasets. Of note…...Cuffmerge works fine when the Gencode GTF is omitted as a reference genome. CuffCompare also works fine when the same Gencode GTF is used as a reference genome. Presumably there is something wrong with the Cuffmerge set-up relating to the reference genome? Or am I doing something wrong. Best wishes Mark

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Re: [galaxy-user] problems with MAF alignment file in Galaxy
by Jennifer Jackson 16 May '14

16 May '14

Hi Amit, The problem has to do with the MAF files themselves - they are truncated. This occurs when MAF data is extracted from the Table browser (or any data in excess of ~100k lines). This data greatly exceeds that: *Database:*dm3 *Primary Table:*multiz15way *Row Count:*1,633,505 The ends of both dataset #1 and dataset #3 have this warning: --------------------------------------------------------------------------- procedures have exceeded timeout: 1200 seconds, function has ended. --------------------------------------------------------------------------- Instead, you have two options: 1 - obtain the MAF files from the UCSC downloads area. Go to http://genome.ucsc.edu, then in the left blue side bar select "Downloads", then navigate to the data for dm3. The multiz (MAF) will be under the Conservation track data. 2 - this same MAF data is cashed as a local data source on usegalaxy.org. If you queried the blocks using an interval/bed file of coordinates (assigned with database "dm3"), you could obtain the intervals that way. UCSC has the chromsome names and lengths on the D. Mel home page in a table found by clicking on the link near the top named "Sequences". Simple files from this info can be pasted into the "Get Data -> Upload file" tool form to create one-line query datasets, like this one: I was able to run " Extract MAF blocks" then "MAF to Interval" with no problems. I don't know if doing this one chromosome at time is required, but it certainly will work and not exceed any resources. I suggested doing this once, building a workflow, then running on the rest in batch. Hopefully one of these options works out for you! Jen Galaxy team On 5/16/14 6:59 AM, Amit Pande wrote: > Dear Jennifer, > > I uploaded the data both the ways i.e via the FTP and through the UCSC > browser, but all the attempts to extract MAF blocks between insect > species has failed. > I need your help in this regard, so I have shared my history with you. > warm regards, > Amit. > > > On Thu, May 15, 2014 at 5:07 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi Amit, > > This is occurring when you are uploading a MAF "multizXXway" file > obtained from UCSC downloads (genome.ucsc.edu > <http://genome.ucsc.edu>) to Galaxy main (usegalaxy.org > <http://usegalaxy.org>)? Upload using FTP? > https://wiki.galaxyproject.org/Support#Loading_data > > The table browser is generally a poor choice to extract more than > a few regions with MAF data (per query) as there are limits on how > many lines of output will be sent over. Incomplete transfers are a > common. This error could be related to a format or datatype > assignment issue from that type of issue. > > Please give FTP loading a try if you have not already. Then if > problems continue, you can share a history link with me. Note > which dataset was the MAF uploaded via FTP. This is how to share: > https://wiki.galaxyproject.org/Learn/Share > > Best, > > Jen > Galaxy team > > Going forward, please ask questions on our new forum that is > replacing this list (very soon now): > https://wiki.galaxyproject.org/Support#Biostar > > > On 5/14/14 10:52 PM, Amit Pande wrote: >> Dear Galaxy, >> >> I am trying to import a multiz alignment file for all the insect >> species from the UCSC >> genome browser. >> Galaxy does not recognize number of blocks in the multiz file as >> there is a question mark in the file format view (? blocks). >> Then when I am trying to use the tool ( Extract MAF blocks >> <https://usegalaxy.org/tool_runner?tool_id=Interval2Maf1> given a >> set of genomic intervals) then there is an error saying >> >> "An error occurred with this dataset:191757 MAF blocks converted >> to Genomic Intervals for species dm3. There was a problem >> processing your input: exceptions must be old-style classes or >> derived from BaseException, not str" and even when the tool runs >> it shows the following message " >> This is a new dataset and not all of its data are available yet " >> >> Please look into the problem. >> >> warm regards, >> Amit. >> >> >> ___________________________________________________________ >> The Galaxy User List is being replaced by the Galaxy Biostar >> User Support Forum athttps://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/ > > -- > Jennifer Hillman-Jackson > http://galaxyproject.org > > -- Jennifer Hillman-Jackson http://galaxyproject.org

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cuffcompare MPI error
by Antoine Buetti-Dinh 16 May '14

16 May '14

Hi, sorry to bother but now it's the 3rd time I get a message saying that if the problem persists I should contact the galaxy staff. It occurs while running cuffcompare of total RNA to a genomic reference that I uploaded myself (Sulfolobus acidocaldarius). It's about MPI processes terminated incorrectly if I understood it correctly. Just to let you know... These are the details of the generated error: --------------------------------------------------------------- user username twincacca quota_percent 32 total_disk_usage 86918246471 nice_total_disk_usage 80.9 GB email antoine.buetti(a)lnu.se is_admin false tags_used model_class User id 3e934cb0877d45db source HDACollection(8fb8cc6fa23b1dbe,99) xhr readyState 4 responseText {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0} responseJSON err_msg Uncaught exception in exposed API method: err_code 0 status 500 statusText Internal Server Error responseHeaders Server nginx/1.4.7 Date Fri, 16 May 2014 08:58:57 GMT Content-Type application/json Transfer-Encoding chunked Connection keep-alive Cache-Control max-age=0,no-cache,no-store options data parse true emulateHTTP false emulateJSON false ---------------------------------------------------------------END

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galaxy-user May 2014