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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 21 May '14

21 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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Re: [galaxy-user] edit file in galaxy
by Ay Ayy 16 May '14

16 May '14

過去18年力抗抑鬱病折磨，時刻鼓勵自己努力、加油的女子，終因難敵頭痛失眠，昨午在灣仔軒尼詩道向上班僅兩個月的餐廳請辭後，突由大廈31樓天台躍下，身體倒插在餐廳窗外的大廈一樓玻璃簷篷，消防員到場將她救下送院，證實死亡。難敵抑鬱辭職即跳樓死者鍾巧盈（28歲），暱稱小巧，生前與父母及兩名胞妹同住香港仔華貴邨，兩個月前獲軒尼詩道彰顯大廈一樓樂農素食餐廳聘任兼職收銀員。據悉，小巧10歲那年患上抑鬱症，多年來飽受折磨，需經常往醫院接受治療。但她性格樂天，一旦身體狀況不錯，便外出工作，早前曾在一家精品店工作。消息稱小巧最近病情反覆，連續多日頭痛失眠，昨晨11時上班後，向經理辭職。下午2時半落場時她又頭痛不適，經理批准她即時離職休養。怎料，小巧離開餐廳25分鐘後，即被人發現從大廈高處墮下，身體倒插在餐廳對開玻璃簷篷上，嚇得途人立即報警，消防員將她救下送院，但證實不治。 ■鍾巧盈（小圖）3月22日在facebook留言，不但鼓勵自己，更勉勵想自殺的朋友要找尋自己的希望。小巧母親趕往醫院，傷心痛哭。警方相信事件無可疑。小巧任職的樂農是本港首家社會企業素食餐廳，經理說小巧對人有禮，對她去世感惋惜。資料顯示，去年約6,700名兒童及青少年患抑鬱等精神病，醫生指有年輕化趨勢。 Ibrahim YU; wilson (cuhk) ay73ay(a)aol.com Find me at about.me/uy73 -----Original Message----- From: Koehorst, Jasper <jasper.koehorst(a)wur.nl> To: galaxy-user <galaxy-user(a)lists.bx.psu.edu> Sent: Tue, May 13, 2014 3:18 pm Subject: [galaxy-user] edit file in galaxy Koehorst, Jasper (jasper.koehorst(a)wur.nl) is not on your Guest List | Approve sender | Approve domain Hello, I am generating files but sometimes I want to add something to the text file generated. I would like to do this within galaxy instead of downloading, modifying, uploading the file. Is this possible? Thanks, jasper ___________________________________________________________ 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/

2 1

problems with MAF alignment file in Galaxy
by Amit Pande 15 May '14

15 May '14

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.

2 1

edit file in galaxy
by Koehorst, Jasper 13 May '14

13 May '14

Hello, I am generating files but sometimes I want to add something to the text file generated. I would like to do this within galaxy instead of downloading, modifying, uploading the file. Is this possible? Thanks, jasper

3 2

When will megablast be working again
by Scott W. Tighe 28 Apr '14

28 Apr '14

Dear NCBI and Galaxy Team I have sent a note to determine when the Megablast option will be active again. Whether you use Galaxy or NCBI directly, it is inoperative. Scott -- Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999-6666 (cell)

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Megablast database identity
by Scott W. Tighe 28 Apr '14

28 Apr '14

Jennifer I am megablasting a simple 500,000 line dataset that is certainly in galaxy fasta. For a week i have been seeing numerous errors. So i have reprocesed the data multiple times. The error message is "could not find specified database directory" Is there an alternative approach? I did try ncbi directly and that failed too. They say they have a database issue Scott Tighe Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999-6666 (cell)

2 1

"Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened
by Sarah Maman 25 Apr '14

25 Apr '14

Hello, I try to use "Intersect multiple sorted BED files" tool without success. A genome_test have been added in galaxy (genome_test.len in galaxy-dist/tool-data/shared/ucsc/chrom/, .fa and .dict added in .loc fils in tool-data/) but "Intersect multiple sorted BED files" gives this error message : An error occurred running this job: /Epilog : job finished at lun. mars 24 15:55:04 CET 2014 Error: The requested genome file (/..../galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len) could not be opened. Exiting! So, /I have integrated the code modification submitted in Galaxy Central (https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a371…): - chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) + chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey ) But I always have the same error message. Could you please help us ? Thanks in advance, Sarah // -- --*-- Sarah Maman INRA - GenPhySE - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

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