[galaxy-user] FW: [galaxy-bugs] Galaxy tool error report from b...@leeds.ac.uk
Hi Jen, thanks. I am a bit confused: on Galaxy the only human genome listed is hg_g1k_v37. So when I uploaded the new data from Get data, under Genome I selected hg_g1k_v37 Now, all i want is to get cufflinks with gene names: which genome am I supposed to use? the only one I knew was hg19 from iGenomes...but seems i cannot use it. Do I have to select a genome when I upload raw fastq data? I havent stated doign anything so far, its just raw data Thanks a lot, Irene From: Jennifer Jackson [j...@bx.psu.edu] Sent: Wednesday, November 27, 2013 10:08 PM To: Irene Bassano Cc: galaxy-b...@bx.psu.edu Subject: Re: [galaxy-bugs] Galaxy tool error report from b...@leeds.ac.uk Hello, iGenomes covers the UCSC build, and this named Human Feb. 2009 (GRCh37/hg19) (hg19) in the full name in the UI. The hg19 key is the important part - as the name may be abbreviated in some tools, but this key will be in all. The genome with the hg_g1k_v37 key is slightly different and you will have another genome mismatch problem with the RNA-seq (and most other) tools if you combine this genome with data from UCSC (the source of hg19) or the wrong iGenomes file. hg_g1k_v37 (source: 1000 genomes via GATK) and hg19 (source: UCSC) are just about the same, but the identifiers are different. If you want to examine the differences, both are available on our rsync server and can be downloaded and compared. On the Help - Support wiki are links for reference genomes. The iGenomes GTF file for hg19 is on the public Main server, if that is more convenient for you, or should you just want to be sure you have the right one. Look in Shared Data - Data Libraries - iGenomes. Best, Jen Galaxy team ps. please try to send new questions to one of our lists, thanks! On 11/27/13 12:51 PM, Irene Bassano wrote: Hi Jen, I uploaded some fastq files and selected as Genome from the drop down list Homo sapiens b37(hg_g1k_v37). Is this the same as the genome listed in UCSC February 2009 (GRCh37/hg19)? I am using iGenomes to get the gene names rather than annotation such as NM_00 and I fused the UCSC website choosing the newest genome, February 2009 Thanks, best, Irene From: Jennifer Jackson [j...@bx.psu.edu] Sent: Monday, November 18, 2013 7:26 PM To: galaxy-b...@bx.psu.edu; Irene Bassano Subject: Re: [galaxy-bugs] Galaxy tool error report from b...@leeds.ac.uk Hi again, The database mismatch is a problem here is well for the same reasons. My guess is that you intended to run dataset #21 against hg19, and that the run against hg18 was a tool form input mistake? Good luck with the next runs, Jen Galaxy team On 11/18/13 5:21 AM, galaxy-b...@bx.psu.edu wrote: GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the server usegalaxy.org - This is in reference to dataset id 7081835 from history id 1686699 - You should be able to view the history containing the related history item 37: Cufflinks on data 21 and data 34: assembled transcripts by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. usegalaxy.org/history/view?id=d88c1ef77619eb4f - The user 'b...@leeds.ac.uk' provided the following information: Same as before but the reference genome is UCSC MAin on Human:refFlat - job id: 6096851 tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6 job pid or drm id: 136948 - job command line: python /galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/b01956f26c36/cufflinks/cufflinks_wrapper.py --input=/galaxy-repl/main/files/007/074/dataset_7074022.dat --assembled-isoforms-output=/galaxy-repl/main/files/007/081/dataset_7081835.dat --num-threads=8 -I 30 -F 0.1 -j 0.15 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -N -b --ref_file=None --dbkey=hg18 --index_dir=/galaxy/main/server/tool-data -u - job stderr: Error running cufflinks. return code = 1 Command line: cufflinks -q --no-update-check -I 30 -F 0.10 -j 0.15 -p 8 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -u -N -b /galaxy/data/hg18/sam_index/hg18.fa
[galaxy-user] human genome latest annotaiton
Hi Jen, I uploaded some fastq files and selected as Genome from the drop down list Homo sapiens b37(hg_g1k_v37). Is this the same as the genome listed in UCSC February 2009 (GRCh37/hg19)? I am using iGenomes to get the gene names rather than annotation such as NM_00 and I fused the UCSC website choosing the newest genome, February 2009 Thanks, (sorry, I think i sent a mail to bugs report by mistake) best, Irene ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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 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/
Re: [galaxy-user] FW: Tophat/Cuff parameters
Thanks a lot Jen! Irene From: Jennifer Jackson [j...@bx.psu.edu] Sent: Saturday, November 16, 2013 6:57 PM To: Irene Bassano Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] FW: Tophat/Cuff parameters Hi, Yes, the .py part of the wrapper you attached is how the tool is implemented in Galaxy. The .xml is what is displayed on the tool form. Together, these execute the command string for the job. Knowing the parameters used for a job run is definitely important and this is included in the interface. If you click on the info icon, the small circle i, for a dataset, the full command line is listed. Parameters set by the run are listed and can be compared to the manual. Anything not in the command string would be at default, just as if you were running the tool on the command line (not through Galaxy). This information captures execution parameters for reproducibility. Directly from the Galaxy run, but you can also use similar if you choose to run the tool on the command line (to use/add parameters not yet implemented in a Galaxy tool repository). There are a few tools that do not report the command line yet in the interface (older ones), but it can still be obtained independently by triggering an error, then submitting a bug report - a cc copy is sent to the reporter that contains it. Just put in the comments to ignore the bug submission. Not an ideal method (will be addressed), but is open for anyone to use, any tool. Hopefully this helps! No parameters are hidden to my knowledge. Best, Jen Galaxy team On Nov 16, 2013, at 2:44 AM, Irene Bassano b...@leeds.ac.ukmailto:b...@leeds.ac.uk wrote: Thanks again Jen, I just would like to get this point: if I want to modify them then I won’t be using Galaxy right, since there are few of them I can modify. All I would like to know is: are the hidden/chosen/not accessible parameters CHOSEN by Galaxy? If yes, is there any chance to know what has been chosen for these parameters which are not visible? Or did I understand that are default as written in the manual? Hope it’s clear, sorry for insisting but I need to know as I am doing an analysis for someone else and have to report all the options I have opted for! I cannot tell anything about those which are not listed I have read the link you sent me , but I cannot find all the missing options…I opened all the links on it an found only those already listed in the main cufflinks running page(see attachment).. Thanks again for your patience, Best, Irene From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: 15 November 2013 20:59 To: Irene Bassano; 'galaxy-u...@bx.psu.edumailto:galaxy-u...@bx.psu.edu' Subject: Re: [galaxy-user] FW: Tophat/Cuff parameters Hello - Most of these are at defaults. The source code is the best place to find any that are hard-coded (if included, most likely done to manage resources). Again, any of of this could be modified if you have programming resource. The repository is owned by the devteam and in the Tool Shed, search with cuff here: http://usegalaxy.org/toolshed Best, Jen Galaxy team On 11/15/13 2:59 AM, Irene Bassano wrote: Hi Jen, Thanks again. Just to make it clear: if all the options are not present on galaxy but only some of them, does this mean that the absent ones have been set by galaxy dev? are these to be considered best settings not worth changing? I would like to learn a bit more and “play” with all options but if some of them wont affect the final reaults then is not worth changing them. Thanks, Irene From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: 14 November 2013 21:43 To: galaxy-user Cc: Irene Bassano Subject: Tophat/Cuff parameters Hello, Yes, this is correct, not all parameters can be adjusted in the UI. Many can, especially with Tophat, but not all. The list of implemented parameters that will match the documentation is listed at the bottom of each of these tools. The UI form itself up top may have a slightly different human readable name, but most will include the parameter name -r, etc. To see all of the parameters on the forms: 1. Tophat/2 - open TopHat settings to use: Full parameter list 2. Cufflinks/merge/compare/diff - open or modify any listed on form to see full content This tool is in the Tool Shed (http://usegalaxy.org/toolshed), so if you had programming resource available, then these could certainly be modified. Development questions can go do the galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu mailing list, but really the best place to start is in our wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax http://wiki.galaxyproject.org/Tool%20Shed It would be really helpful if you sent questions directly to the galaxy-u...@bx.psu.edumailto:galaxy-u...@bx.psu.edu mailing list going forward. Thanks, Jen Galaxy team On 11/14/13 1:08 PM, Irene Bassano wrote: Hi Jen, thanks a lot for your reply. I am trying to apply some changes
[galaxy-user] FW: Tophat/Cuff parameters
Hi Jen, Thanks again. Just to make it clear: if all the options are not present on galaxy but only some of them, does this mean that the absent ones have been set by galaxy dev? are these to be considered best settings not worth changing? I would like to learn a bit more and play with all options but if some of them wont affect the final reaults then is not worth changing them. Thanks, Irene From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: 14 November 2013 21:43 To: galaxy-user Cc: Irene Bassano Subject: Tophat/Cuff parameters Hello, Yes, this is correct, not all parameters can be adjusted in the UI. Many can, especially with Tophat, but not all. The list of implemented parameters that will match the documentation is listed at the bottom of each of these tools. The UI form itself up top may have a slightly different human readable name, but most will include the parameter name -r, etc. To see all of the parameters on the forms: 1. Tophat/2 - open TopHat settings to use: Full parameter list 2. Cufflinks/merge/compare/diff - open or modify any listed on form to see full content This tool is in the Tool Shed (http://usegalaxy.org/toolshed), so if you had programming resource available, then these could certainly be modified. Development questions can go do the galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu mailing list, but really the best place to start is in our wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax http://wiki.galaxyproject.org/Tool%20Shed It would be really helpful if you sent questions directly to the galaxy-u...@bx.psu.edumailto:galaxy-u...@bx.psu.edu mailing list going forward. Thanks, Jen Galaxy team On 11/14/13 1:08 PM, Irene Bassano wrote: Hi Jen, thanks a lot for your reply. I am trying to apply some changes to certain parameters in cufflinks. I have read them on the manual but on galaxy are not all listed. is this because they have been chosen already by galaxy and set to certain values you guys believe are optimal? I cannot find for example: Maximum genomic length allowed for a given bundle. Minimum intron size allowed in genome. Minimum average coverage required to attempt 3' trimming. and many others. I also wanted to access full parameters for Tophat and Cuffdiff... Any suggestion on how can I access them? Thanks, Irene -- Jennifer Hillman-Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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 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/
[galaxy-user] cufflinks reference annotation
HI guys, how do we know when to select a refernce annotation when running cufflinks?And if yes, which one from UCSC should we chose: refgene or knowngenes? Thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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 To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] cuffdiff
Hi, just few questions about cuffdiff if anyone can answer: 1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two files 2.what to use as input: cufflinks, cuffcompare or cuffmerge? Thanks a lot! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at 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 To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
