Re: [galaxy-user] Problem with executable file in FastQC
Hi, Jorge, Galaxy source includes the Galaxy interfaces but not the third party executables for tools like fastqc or bwa. They can be automagically installed if you install the tool from a tool shed but at a guess, you are working on your desktop with the fastqc tool in a recent clone of galaxy? Unfortunately, the tool can't run until you have the fastqc software working in a particular way hinted at in the guide for the fastqc tool on the page at http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies - try that please? There are things to do to make your instance more reliable and stable too - eg http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer On Mon, Dec 9, 2013 at 9:48 PM, Jorge Braun braun_...@hotmail.com wrote: Hi mates!! I have a problem with Galaxy... FastQC doesn't run because the file FastQC.py cann't find executable file FastQC.xml. Almost, that file is in the same directory called rgenetics, (seeing Linux terminal) . someone can help me? thanks and have a nice day :) ___ 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] Counts of mapped reads for each gene?
Hi, Yan The htseq_bams_to_count_matrix tool in the test toolshed might be worth a try - it creates tabular count matrices from any number of individual sample bam/sam files (it is NOT read group aware!). Each row contains the count for that contig for each sample. It uses HTSeq code and you supply your favourite gene model as a GTF file for defining the regions to count and how to amalgamate - eg count reads overlapping exons and sum those into total counts for each gene. Please give it a try. Install from the admin interface and let me know how you get on. There's a companion tool differential_count_models also in the test toolshed that includes edgeR, DESeq2 and VOOM from Bioconductor - it runs 1 or 2 way GLMs using the count matrices generated by the htseq tool - be warned that it takes a long time to install everything so be patient and allow 20 minutes or so for the installation to finish because it compiles and installs R 3.0.1 and Bioconductor packages. Suggestions for improvement or bug reports always welcomed. Good luck. On Thu, Aug 22, 2013 at 3:35 PM, Yan He yanh...@hotmail.com wrote: Hi Jen and other galaxy-users, ** ** I am analyzing our RNA-seq data. First, I mapped the RNA-seq data to the reference genome. I am wondering if there is a tool that could count the number of reads that mapped to each gene. That’s important information for my subsequent analysis. Any reply is highly appreciated! Thanks, ** ** Yan ___ 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/ ___ 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] Rename tool output file in Galaxy
Sachit, that's a feature, not a bug. Changing the name of a file on disk being managed by Galaxy is unlikely to have a happy ending. The pencil icon allows changes to the history display name but the disk file name needs to be left alone. On Wed, Jul 24, 2013 at 8:15 PM, Sachit Adhikari sachit.techner...@gmail.com wrote: Yes, but unfortunately that didn't work too. I have already tried the solution you provided. I could edit the tags and annotations but it won't change the file name in my file system. The file is still named as * dataset_43649.dat. * On Wed, Jul 24, 2013 at 3:52 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Jul 24, 2013 at 10:35 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: Hi, By i do you mean Edit attributes button? There are four sub-headings on that: Attributes, Convert format, Datatype and permissions but I can't see data file's full path on any of them. What's wrong? No, not the edit button. First click on a dataset's title so it expands. You should see a snippet of data etc plus a row of icons (save, information, reload in bottom left of the history, and tags and annotation bottom right). Peter ___ 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/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ 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] Exceptionally high RPKM values of miRNA and other short genes in Cuffdiff's output
Hi, Thanh, If your primary goal is inference about differential 'gene' expression taking biological variability into account with biological replicates for each of two conditions, you might want (eg see Dillies et al., http://bib.oxfordjournals.org/content/early/2012/09/15/bib.bbs046.long and http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FAbstracts.2FPosters.P4:_Comparing_R-based_methods_and_Cuffdiff2_for_analysis_of_RNA-seq_data_in_Galaxy) to try (and compare!) edgeR (and optionally DESeq and VOOM/limma). A set of *very much beta* tools is available for admin installation and user testing from the test toolshed in the statistics section owned by fubar. The edgeR tool can optionally run 2 way GLM. It requires raw count matrices as inputs which can be generated from a GTF/'gene' model of your choice and any number of mapped SAM/BAM inputs using the htseq based companion tool in the same tool shed section. Please don't install to a production machine yet but we're getting good results from it - feedback and code improvements are welcomed from willing beta testers. The R 3.0.x tool shed dependency package in particular is still under development and is likely to change substantially in the next week or two as we sort out a sane and generalised Atlas dependency installation. On Fri, Jul 19, 2013 at 2:55 AM, Hoang, Thanh hoan...@miamioh.edu wrote: Hi all, I have been analyzing my RNA-seq data on mouse tissues. My RNA-data is single-ended and 51 bp in length. I ran TopHat/Cufflink/Cuffdiff to test to differential gene expression In the Cuffdiff's output, I got very high RPKM value for some of miRNA and some other short genes ( less than 100bp). These genes are in the top genes with the highest RPKM. I think the RPKM values of these genes are probably too high to be true. *test_id* *gene_id* *gene* *locus* *sample_1* *sample_2* *status* * value_1* *value_2* *log2(fold_change)* *test_stat* *p_value* *q_value* * significant* *ENSMUSG0093077* *ENSMUSG0093077* *Mir5105* * 5:146231229-146302874* *Epithelium* *Fiber* *OK* *1.53E+06* * 445558* * -1.78097* *-355.367* *0.00715* *0.016986* *yes* *ENSMUSG0093098* * ENSMUSG0093098* *Gm22641* *7:130162450-133124354* *Epithelium* *Fiber* *OK* *87894.1* * 36474.7* *-1.26887* *-0.59863* *0.4913* *0.587174* *no* *ENSMUSG0089855* *ENSMUSG0089855* *Gm15662* * 10:105187662-105583874* *Epithelium* *Fiber* *OK* *42868.9* * 21566.5* * -0.99114* *-20.7066* *0.0186* *0.039568* *yes* *ENSMUSG0092984* * ENSMUSG0092984* *Mir5115* *2:73012853-73012927* *Epithelium* *Fiber* * OK* *21104.8* * 8317.49* *-1.34335* *-447.314* *0.0001* *0.000354* *yes* *ENSMUSG0086324* *ENSMUSG0086324* *Gm15564* *16:35926510-36037131* *Epithelium* *Fiber* *OK* *6443.35* * 3664.15* *-0.81433* *-1.52095* * 0.2129* *0.301429* *no* *ENSMUSG0092981* *ENSMUSG0092981* * Mir5125* *17:23803186-23824739* *Epithelium* *Fiber* *OK* *5974.14* * 2390.75* *-1.32127* *-0.34111* *0.5746* *0.661937* *no* I checked some forums and they said that this is the drawback of TopHat/Cufflink/Cuffdiff when dealing with short genes. But I am still not so clear about this. Anyone got the same problem? What can I do with this situation? Anyone suggests any other good tools to test for (1) differential gene expression OR (2) both differential gene expression and gene discovery? Thank you Thanh ___ 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] Upload files from filesystem paths
Hi, Neal, Thanks - that sounds interesting. Like I said, composite datatypes are designed to manage collections of related files as a unit and this sounds like a potential use case. There are lots of tools and lots of code that can serve as examples but it's definitely not trivial because you will almost certainly be subclassing the Html data class and writing methods to manage those related files (ie extending the guts of Galaxy) and your tools will all need to know how to deal with the managed structure when they get one as an input. You may need to find or build up a programmer with some relevant Galaxy composite datatype experience. There is some documentation but it's not extensive or transparent. Good luck. On Fri, Jan 4, 2013 at 9:19 AM, neil.burd...@csiro.au wrote: Hi Ross, I don’t know of any tools that work in the way I want, but I’m not an expert on tools within Galaxy. Essentially the data in the directories will be fixed. We run a tool from Galaxy that generates some output data, this data then “checks” the data located under the directories I am trying to upload to Galaxy. There will probably be around 20 directories, and the data produced would then search these directories looking for “a closest match” once located it would use the remaining files in the directory to complete the process. ** ** So for example, the application is segmenting an image, so a part of the image is the output. This is compared with files in the uploaded directories and a file in a particular directory is chosen (as the closest match) then the remaining files in the directory are then used to complete the process. ** ** Does that make sense? There would be around 20 files in each directory.*** * ** ** Thanks Neil ** ** *From:* Ross [mailto:ross.laza...@gmail.com] *Sent:* Thursday, 3 January 2013 2:24 PM *To:* Burdett, Neil (ICT Centre, Herston - RBWH) *Cc:* galaxy-user *Subject:* Re: [galaxy-user] Upload files from filesystem paths ** ** Neil, It would help if you could point to an existing tool that works the way you want. I don't know of any that deal with arbitrary nested directories containing arbitrary files. A new composite datatype could impose a structure that a tool could be written to deal with (eg the pbed datatype used in some rgenetics tools) but arbitrary data structures are not going to be possible AFAIK. You're unlikely to get useful help without a much more complete and clear explanation of the problem. ** ** ** ** On Thu, Jan 3, 2013 at 1:50 PM, neil.burd...@csiro.au wrote: Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt Under the Upload files from filesystem paths, In the path to upload window I paste /home/galaxy/data-test. This then puts the somefile.txt in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to keep the directory structure. I can see this if I navigate through the shared data tab but where is this information stored under the galaxt-dist structure. As my application needs to have the directory structure kept, so need to access it from the xml/command line I thought it might have been something like: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. But this is not the case rather /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory structure. So how can I access this information from the xml files in the tools directory? Thanks Neil From: Ross [ross.laza...@gmail.com] Sent: Wednesday, January 02, 2013 4:43 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39 AM, neil.burd...@csiro.aumailto: neil.burd...@csiro.au wrote: Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ** ** ___ 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
Re: [galaxy-user] Upload files from filesystem paths
For the simplest case, start with the tools/rgenetics/rgFastQC tool - it doesn't need a subclass but uses the Html datatype files_path as a simple multiple file bucket. Once you've got that all figured out, check out the rgenetics datatypes (eg pbed) subclassed from Html defined in lib/galaxy/datatypes/genetics and the tools that use it (eg TDT or CaCo tools) in tools/rgenetics for more complex hackery keeping related files needed by plink together. On Fri, Jan 4, 2013 at 9:50 AM, neil.burd...@csiro.au wrote: Thanks for the help Ross. ** ** Any chance you can point me to the examples you mentioned? ** ** Thanks again Neil ** ** *From:* Ross [mailto:ross.laza...@gmail.com] *Sent:* Friday, 4 January 2013 8:35 AM *To:* Burdett, Neil (ICT Centre, Herston - RBWH) *Cc:* galaxy-user *Subject:* Re: [galaxy-user] Upload files from filesystem paths ** ** Hi, Neal, Thanks - that sounds interesting. Like I said, composite datatypes are designed to manage collections of related files as a unit and this sounds like a potential use case. There are lots of tools and lots of code that can serve as examples but it's definitely not trivial because you will almost certainly be subclassing the Html data class and writing methods to manage those related files (ie extending the guts of Galaxy) and your tools will all need to know how to deal with the managed structure when they get one as an input. ** ** You may need to find or build up a programmer with some relevant Galaxy composite datatype experience. There is some documentation but it's not extensive or transparent. ** ** Good luck. ** ** On Fri, Jan 4, 2013 at 9:19 AM, neil.burd...@csiro.au wrote: Hi Ross, I don’t know of any tools that work in the way I want, but I’m not an expert on tools within Galaxy. Essentially the data in the directories will be fixed. We run a tool from Galaxy that generates some output data, this data then “checks” the data located under the directories I am trying to upload to Galaxy. There will probably be around 20 directories, and the data produced would then search these directories looking for “a closest match” once located it would use the remaining files in the directory to complete the process. So for example, the application is segmenting an image, so a part of the image is the output. This is compared with files in the uploaded directories and a file in a particular directory is chosen (as the closest match) then the remaining files in the directory are then used to complete the process. Does that make sense? There would be around 20 files in each directory.*** * Thanks Neil *From:* Ross [mailto:ross.laza...@gmail.com] *Sent:* Thursday, 3 January 2013 2:24 PM *To:* Burdett, Neil (ICT Centre, Herston - RBWH) *Cc:* galaxy-user *Subject:* Re: [galaxy-user] Upload files from filesystem paths Neil, It would help if you could point to an existing tool that works the way you want. I don't know of any that deal with arbitrary nested directories containing arbitrary files. A new composite datatype could impose a structure that a tool could be written to deal with (eg the pbed datatype used in some rgenetics tools) but arbitrary data structures are not going to be possible AFAIK. You're unlikely to get useful help without a much more complete and clear explanation of the problem. On Thu, Jan 3, 2013 at 1:50 PM, neil.burd...@csiro.au wrote: Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt Under the Upload files from filesystem paths, In the path to upload window I paste /home/galaxy/data-test. This then puts the somefile.txt in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to keep the directory structure. I can see this if I navigate through the shared data tab but where is this information stored under the galaxt-dist structure. As my application needs to have the directory structure kept, so need to access it from the xml/command line I thought it might have been something like: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. But this is not the case rather /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory structure. So how can I access this information from the xml files in the tools directory? Thanks Neil From: Ross [ross.laza...@gmail.com] Sent: Wednesday, January 02, 2013 4:43 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39
Re: [galaxy-user] Upload files from filesystem paths
Neil, It would help if you could point to an existing tool that works the way you want. I don't know of any that deal with arbitrary nested directories containing arbitrary files. A new composite datatype could impose a structure that a tool could be written to deal with (eg the pbed datatype used in some rgenetics tools) but arbitrary data structures are not going to be possible AFAIK. You're unlikely to get useful help without a much more complete and clear explanation of the problem. On Thu, Jan 3, 2013 at 1:50 PM, neil.burd...@csiro.au wrote: Hi Ross, I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt Under the Upload files from filesystem paths, In the path to upload window I paste /home/galaxy/data-test. This then puts the somefile.txt in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to keep the directory structure. I can see this if I navigate through the shared data tab but where is this information stored under the galaxt-dist structure. As my application needs to have the directory structure kept, so need to access it from the xml/command line I thought it might have been something like: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. But this is not the case rather /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory structure. So how can I access this information from the xml files in the tools directory? Thanks Neil From: Ross [ross.laza...@gmail.com] Sent: Wednesday, January 02, 2013 4:43 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: galaxy-user Subject: Re: [galaxy-user] Upload files from filesystem paths Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39 AM, neil.burd...@csiro.aumailto: neil.burd...@csiro.au wrote: Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ 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/
Re: [galaxy-user] Upload files from filesystem paths
Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them. On Wed, Jan 2, 2013 at 11:39 AM, neil.burd...@csiro.au wrote: Hi, I have a local galaxy installation. I've created a data library, selected Upload files from filesystem paths, pasted a path in the path to upload window, and I've selected to preserve the directory structure. And the files get imported. How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure Thanks for any help Neil ___ 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/
Re: [galaxy-user] Identification of replicate outlier
Hi Dave, This is an interesting and non-trivial question that extends well beyond Galaxy - and there's no simple solution AFAIK Defining an 'outlier' tends to boil down to subjective judgement in most real cases I've seen. EG: see http://comments.gmane.org/gmane.science.biology.informatics.conductor/40927 My 2c worth: a) confirm that all of your sample library sizes and quality score distributions are comparable with the FastQC tool. A sample with relatively low library size may indicate an upstream technical failure with (eg) RNA extraction or a flowcell lane. b) check that the number of unique alignments to the reference are similar (eg picard alignment summary metrics or even the samtools flagstat tool) c) if you can create an appropriate input matrix (read counts by exon or other contig for each sample eg), the Principal Component Analysis tool might be helpful (library size normalization is one devil that lies in the detail and it's not quite the same as MDS - see below) d) If you're an R hacker, you might find http://gettinggeneticsdone.blogspot.com.au/2012/09/deseq-vs-edger-comparison.html useful - it shows how to get MDS plots which are probably the most reliable way to identify samples that don't cluster well with the other members of their tribe On Fri, Nov 9, 2012 at 10:22 AM, Dave Corney dcor...@princeton.edu wrote: Hello list, I've been analyzing an experiment with two groups each with three replicates. My workflow was TopHat (paired end) - Cufflinks - CuffDiff. Unfortunately, there are not many significant differences identified by CuffDiff. I am wondering whether one of my replicates might be an outlier. Does anybody have a suggestion on how to search for an outlier? The quality statistics of the unprocessed data looked equally good for all samples, so I don't think that this is a problem. Thanks, Dave ___ 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/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ 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/
Re: [galaxy-user] RSEM on Galaxy
Alicia, Some relevant details usually make it easier for list members to help you - please see http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions Did you load the offending tool from a toolshed or is it a tool wrapper you wrote yourself? If the latter, I have two suggestions: 1) Search paster.log for your tool name and make sure it got correctly loaded when you restarted Galaxy - xml syntax errors like misplaced characters will break the tool loading process. 2) if the log shows that it loaded, make sure you refresh the tool frame in your browser after restarting Galaxy - eg clicking the analyse data tab will get rid of the old cached copy. On Sat, Oct 6, 2012 at 10:02 AM, Alicia R. Pérez-Porro alicia.r.perezpo...@gmail.com wrote: Hi all, Recently i installed RSEM into Galaxy. The problem is that now i cannot find the tool when i open my galaxy in my computer. I checked and rsem folder is inside the tool folder. Any suggestions? Thanks, Alicia. -- Alicia R. Pérez-Porro PhD student Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/ Department of Marine Ecology Center for Advanced Studies of Blanes (CEAB-CSIC) C/Accés Cala St. Francesc 14 17300 Blanes, Girona, SPAIN phone: +34 972 336 101 fax: +34 972 337 806 www.ceab.csic.es ___ 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/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ 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/
Re: [galaxy-user] Cuffdiff no without replicates
On Wed, Oct 3, 2012 at 9:11 PM, i b ibse...@gmail.com wrote: Dear all, how reliable is running Cuffdiff without replicates? e.g.one samples agains another one? Is it statistically makign any difference when using replicates? Seqanswers might be a better place to ask this very interesting technical question that goes way beyond Galaxy... My 2c: Statistically speaking, sequencing and biology are both noisy. Replicates provide information about non-experimental (technical and biological) variation. That variation is usually not the variation you are looking for, but if you want to remove it, you have to model it and that requires information from replicates (or really good guesswork). In some situations (eg extreme experimental conditions), I'm sure you'll find biologically meaningful signal without them but in my experience, they can really help to decrease non-experimental noise, particularly where the experimental condition induces only subtle changes in transcript abundance. You could always analyse a data set with replicates and compare the results with and without those replicates yourself to see what happens - it would be a nice paper I'm sure. 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/
Re: [galaxy-user] Bam to Fastq conversion
There's a picard sam to fastq converter which AFAIK works on bams too: https://main.g2.bx.psu.edu/tool_runner?tool_id=picard_SamToFastq On Sat, May 26, 2012 at 9:48 AM, William M. Strauss cyclotouri...@mac.com wrote: I have a bunch of BAM files that I need to convert to FASTQ, are there such tools in Galaxy? ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-user] Alignment coordinates
Erika, Although Galaxy doesn't have a suitable mapping tool for fasta format sequences, you can use the Galaxy clustalw tool option to output a fasta format file and then upload that fasta file to the ncbi Blast tool at http://blast.ncbi.nlm.nih.gov/Blast.cgi to find where the sequences align - blast allows mapping of sequences on multiple organisms. I hope this helps in your research On Fri, Apr 13, 2012 at 10:36 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Erika, Unfortunately, Galaxy does not have a parser tool to transform clustal datatypes into tab-coordinate based files. Sorry we couldn't help! Best, Jen Galaxy team On 4/12/12 8:07 AM, Erika Kruse wrote: Hello, I imported a sequence alignment file from clustalw. How can I generate a list of the coordinates of the matching regions? Thank you. Erika ___ 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/ ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-user] Quick question on generated tables
Hi, Carly. Hover your mouse pointer over the little floppy disk icon and the help text 'download' should appear - click the icon to download the contents of the file to your local workstation. It's an interval file so it will be tab delimited and should open easily in your favourite spreadsheet program. Glad to hear you're enjoying using Galaxy - I hope this helps you get your work done On Wed, Mar 14, 2012 at 9:54 AM, Carly Hom carlyho...@gmail.com wrote: Hello, I am working on a project that involves extracting a list of promoter regions that contain a significant enough H3k27me3 signal. So far I have produced an output in the ENCODE genome browser which is great for the visual representations I will be needed, but I also need to extract the table that was generated. I see the first few lines in a snapshot of the data that galaxy provided me with, but how do I extract that entire table into spreadsheet or txt format? If you could enlighten me on a galaxy ___ 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/
Re: [galaxy-user] Problems starting Galaxy Cloudman
-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg, /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload Traceback (most recent call last): File /mnt/galaxyTools/galaxy-central/lib/galaxy/web/buildapp.py, line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/app.py, line 24, in __init__ self.config.check() File /mnt/galaxyTools/galaxy-central/lib/galaxy/config.py, line 243, in check tree = parse_xml( config_filename ) File /mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py, line 105, in parse_xml tree = ElementTree.parse(fname) File /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py, line 576, in parse source = open(source, rb) IOError: [Errno 2] No such file or directory: './migrated_tools_conf.xml' Removing PID file paster.pid While I'm here, I see a new Galaxy Cloudman AMI 072133624695/galaxy-cloudman-2012-02-26. I can't manage to start that, I get an error as below, with all types of instance, (tiny/small/medium/large). Is that a recommended AMI now ? It would be good to have a new updated AMI. snap1.png Thanks ! -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-user] RE : % On-Off target
Hi Antoine. Thanks - sorry, I haven't analysed that particular platform - anyone? http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics seems comprehensive... Why not try the Galaxy picard Hybrid Selection metrics tool on your data? On Wed, Dec 21, 2011 at 6:25 PM, Antoine ROUSSELIN a.rousse...@baclesse.fr wrote: Hello, My English is very bad, it's a shame! My I have a file for my baits (create a bed file of your Agilent SureSelect targets with exons and introns captured). Sequencing output, I get the files. Bam, my result sets of alignments on the human genome complete (with CASAVA). I try to get the coverage I only exonic regions (+ or - 50 bp). Thanks ROUSSELIN Antoine Clinical Biology and Oncology Laboratory Centre François BACLESSE France/Caen a.rousse...@baclesse.fr Tel : (33) 02.31.45.40.44 Fax : (33) 02.31.45.50.53 Message d'origine De: Ross [mailto:ross.laza...@gmail.com] Date: mer. 12/21/2011 03:16 À: Antoine ROUSSELIN Cc: galaxy-user@lists.bx.psu.edu Objet : Re: [galaxy-user] % On-Off target Hello Antoine, I'm not sure I really understand your question but if the metrics described at http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics are of use, you could try the picard hybrid selection metrics Galaxy tool or use it on the command line. Otherwise perhaps you can get a more helpful response if you provide a clear explanation of the data formats you have and the measures you want. On Wed, Dec 21, 2011 at 2:59 AM, Antoine ROUSSELIN a.rousse...@baclesse.frwrote: ** hello, I'm looking for a tool (or command line) to determine the % On-Off target + or - 50 bp of exon from my capture file but not annotated (!!!). Capture SureSelect agilent home. Current pipeline: GAIIx Illumina CASAVA1.8 IGV CNV-seq SAMtools BEDtools GALAXY NextGENe Please HELP ROUSSELIN Antoine Clinical Biology and Oncology Laboratory Centre François BACLESSE France/Caen a.rousse...@baclesse.fr Tel : (33) 02.31.45.40.44 Fax : (33) 02.31.45.50.53 ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-user] history was empty
Hi, Weimin, What do you see when you select Options | Saved Histories (top right of the history panel)? If that doesn't show your old histories to re-open, please let us know exactly which galaxy URL you were using and what login name you used so we can take a look. Note that you need to be logged in to the same user account each time for histories to be reliably preserved between sessions. On Tue, Dec 6, 2011 at 12:55 PM, dongdong zhaoweiming zhaoweiming1...@yahoo.com.cn wrote: 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 ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-user] more on varying number of output files in xml
Hi, Nicholas, You'll almost certainly want to write a wrapper to create the plink command line and run it - a wrapper script can construct a correct plink command line and then do all sorts of post-plink transformation on the outputs as needed - which in my experience it usually is. Most of the rgenetics tools do just that so looking at the source under tools/rgenetics may provide some prototypes you can change to suit your needs - eg rgQC.py and rgQC.xml Plink spews out all sorts of stuff so you may want to explore the Html datatype - see http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003311.html for a brief explanation. On Wed, Nov 9, 2011 at 1:31 AM, Nicholas Robinson nicholas.robin...@nofima.no wrote: Hi Galaxy users, I am trying to write a simple tool that sends commands to shell to run Plink (and other analysis packages set up on our Galaxy server). I am new to this, but have managed to write some tools before that work in a similar fashion, at least when you can specify what input and output files will be produced. For plink there are a large number of options and different outputs possible. I have seen the discussion on the user group about how to handle multiple output files (eg. http://lists.bx.psu.edu/pipermail/galaxy-user/2009-September/000743.html). Normally to run plink you specify a single file name (eg. --out $output1) and the program can produce two, to a few, output files (eg depending on the analysis it might produce a $output1.log file and a $output1.cmh file if I do a certain test, otherwise it might produce the log file and two other files). If I add: --out $output1 $output1.id $__new_file_path__ to the command line to try to capture all the output, as suggested for when the interpreter is python, then when I run the tool in galaxy it says: ERROR: Problem parsing the command line arguments. ie. plink makes a fuss about the addition to the command line (I suspect). Have any of you figured out a way to handle varying numbers of multiple output files under these circumstances? Please give me a simple reponse if you can, I am a new user. Cheers, Nick ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-user] Application error
Hi, Sarah. The message you saw: AssertionError: ##rgFastQC.py error - cannot find executable /Users/allabyrg/Desktop/galaxy-dist/tool-data/shared/jars/FastQC/fastqc suggests that the wrapper can't find the required FastQC perl wrapper called fastqc. For complicated reasons, it needs to be available as part of a complete FastQC installation as it calls the various java components and expects to find them where the FastQC distribution puts them. Please try unpacking the FastQC distribution archive into that .../tool-data/shared/jars directory - no galaxy restart required - and see if that helps? On Wed, Nov 9, 2011 at 9:35 AM, Palmer, Sarah s.a.pal...@warwick.ac.uk wrote: Hi, I have been trying to run fastqc on our standalone installations of Galaxy and repeatedly get the attached error message. I have tried this now with both 454 and Illumina fastq files, on 2 different Mac Machines with 10.5 and 10.6 OS and Python versions 2.5 and 2.7 on one of the machines and get the same problem occurring each time. Could you please help me find a fix for this? Cheers, Sarah ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-user] GATK best practices with local installation of Galaxy
Hi, Camille, I can see this really needs a 'proper' fix - preferably taking advantage of the automated header merge. Preserving the metadata from each bam automatically is safer and less error-prone but you could use the existing Replace sam/bam header tool to do the surgery once you have a correct header in SAM format in your history? I'm currently testing changes which replace the current samtools merge code with a call to Picard MergeSamFiles. I'll add a switch to control whether all input headers are merged in case there are situations where it's not wanted. I'll let you know when you can try it out on our test instance and which revision of the galaxy-central repository contains the changes so you can get it working on your local installation. On Wed, Aug 3, 2011 at 11:49 PM, Camille Stephan camille.step...@irbbarcelona.org wrote: Hi Ross, thanks for your answer. I found a dirty fix for merging pairs of bam files, had to change a couple of things in my local installation though. - Add group reads to each BAM file separately using Picard's Add or Replace Groups (with ID=s1 and ID=s2 for each file) - Create the rg.txt file containing something like this: @RG ID:s1 SM:s1 LB:s1 PL:Illumina @RG ID:s2 SM:s2 LB:s2 PL:Illumina Modify sam_merge.py to call: samtools merge -rh path/to/rg.txt %s %s... It works. The problem is all (pairs of) files will end up with the same IDs and labels, unless the rg.txt file is changed every time. Would it be very difficult to add to the Galaxy wrapper the option of creating rg.txt on the fly and adding the -h option to the samtools call? I'm not familiar with creating wrappers for Galaxy, any suggestion as to where to start? Thanks again, Camille On Wed, Aug 3, 2011 at 2:34 PM, Ross ross.laza...@gmail.com wrote: Camille, thanks for reporting this - I think you have found a bug. We definitely need to be able to preserve metadata when we merge bams. Thanks for your suggestion of using mergeSamFiles - yes, I think it might be a good fix for this problem - but it will take a little while and won't reach the Main site for a few weeks once it's done. It is possible to write your own wrapper locally if you need it fast. Sorry for the inconvenience and thanks again. On Wed, Aug 3, 2011 at 6:15 PM, Camille Stephan camille.step...@irbbarcelona.org wrote: Hello guys, I'm trying to run a pipeline of the best practices for snp and indel discovery as described by the people at Broad and I'm running into troubles with the GATK tools in a local installation of Galaxy. The main problem I have is that merging bam files with the samtools merge tool doesn't keep read group for each sample, causing Count Covariates to crash. The pipeline works fine with a single bam file, but I need to realign at least two files at a time. Is there a way to set the read group of a merged bam inside Galaxy? Are there plans to include the merge tool from Picard in Galaxy? Is there an easy way for me to do this locally? (Although I would like to run this in the cloud later on when the workflow is ready). Thanks! Camille -- *** Camille Stephan-Otto Attolini, PhD Senior Research Officer, Bioinformatics and Biostatistics unit IRB Barcelona Tel (+34) 93 402 0553 ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; -- *** Camille Stephan-Otto Attolini, PhD Senior Research Officer, Bioinformatics and Biostatistics unit IRB Barcelona Tel (+34) 93 402 0553 -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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
Re: [galaxy-user] GATK best practices with local installation of Galaxy
Hi, Camille. If you can find some time to upload some of your bam files, could you please test the revised bam merge tool on http://test.g2.bx.psu.edu/ and let me know how you go. This won't be on the main site until the next scheduled update in a few weeks. If you need this locally, the changes are in galaxy-central from where anyone can grab them - the key file you need to update is tools/samtools/sam_merge.xml and you'll also need MergeSamFiles.jar from a recent Picard release to be available in your tool-data/shared/jars directory. Hope this helps - thanks for pointing out the bug. On Thu, Aug 4, 2011 at 12:02 PM, Ross ross.laza...@gmail.com wrote: Hi, Camille, I can see this really needs a 'proper' fix - preferably taking advantage of the automated header merge. Preserving the metadata from each bam automatically is safer and less error-prone but you could use the existing Replace sam/bam header tool to do the surgery once you have a correct header in SAM format in your history? I'm currently testing changes which replace the current samtools merge code with a call to Picard MergeSamFiles. I'll add a switch to control whether all input headers are merged in case there are situations where it's not wanted. I'll let you know when you can try it out on our test instance and which revision of the galaxy-central repository contains the changes so you can get it working on your local installation. On Wed, Aug 3, 2011 at 11:49 PM, Camille Stephan camille.step...@irbbarcelona.org wrote: Hi Ross, thanks for your answer. I found a dirty fix for merging pairs of bam files, had to change a couple of things in my local installation though. - Add group reads to each BAM file separately using Picard's Add or Replace Groups (with ID=s1 and ID=s2 for each file) - Create the rg.txt file containing something like this: @RG ID:s1 SM:s1 LB:s1 PL:Illumina @RG ID:s2 SM:s2 LB:s2 PL:Illumina Modify sam_merge.py to call: samtools merge -rh path/to/rg.txt %s %s... It works. The problem is all (pairs of) files will end up with the same IDs and labels, unless the rg.txt file is changed every time. Would it be very difficult to add to the Galaxy wrapper the option of creating rg.txt on the fly and adding the -h option to the samtools call? I'm not familiar with creating wrappers for Galaxy, any suggestion as to where to start? Thanks again, Camille On Wed, Aug 3, 2011 at 2:34 PM, Ross ross.laza...@gmail.com wrote: Camille, thanks for reporting this - I think you have found a bug. We definitely need to be able to preserve metadata when we merge bams. Thanks for your suggestion of using mergeSamFiles - yes, I think it might be a good fix for this problem - but it will take a little while and won't reach the Main site for a few weeks once it's done. It is possible to write your own wrapper locally if you need it fast. Sorry for the inconvenience and thanks again. On Wed, Aug 3, 2011 at 6:15 PM, Camille Stephan camille.step...@irbbarcelona.org wrote: Hello guys, I'm trying to run a pipeline of the best practices for snp and indel discovery as described by the people at Broad and I'm running into troubles with the GATK tools in a local installation of Galaxy. The main problem I have is that merging bam files with the samtools merge tool doesn't keep read group for each sample, causing Count Covariates to crash. The pipeline works fine with a single bam file, but I need to realign at least two files at a time. Is there a way to set the read group of a merged bam inside Galaxy? Are there plans to include the merge tool from Picard in Galaxy? Is there an easy way for me to do this locally? (Although I would like to run this in the cloud later on when the workflow is ready). Thanks! Camille -- *** Camille Stephan-Otto Attolini, PhD Senior Research Officer, Bioinformatics and Biostatistics unit IRB Barcelona Tel (+34) 93 402 0553 ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; -- *** Camille Stephan-Otto Attolini, PhD Senior Research Officer, Bioinformatics and Biostatistics unit IRB Barcelona Tel (+34) 93 402 0553 -- Ross Lazarus MBBS MPH
Re: [galaxy-user] Weblogo results empty
Holger, thanks for finding those errors - I'll take a look shortly. What's the 'dependency directory' ? I don't think the wrapper knows anything about it. The tool assumes that the weblogo script is on the path when the actual job starts executing - wherever that is. If the weblogo script produces output it must be on the path after you source that script and working I think. So, the environment on the execution node must include the relevant path. Otherwise it won't work. What path does the execution host get when a galaxy job is run? Does it include the right path to that weblogo script (marked executable)? Can the user each job runs as execute it? On Thu, Jul 7, 2011 at 7:56 PM, Holger Klein h.kl...@imb-mainz.de wrote: Hi Ross, On 07/07/2011 02:07 AM, Ross wrote: Please try the new version 0.4 of the weblogo wrapper in galaxy-central #5772 - it has additional error reporting that may help clarify dependency or other problems and let me know how you go? thanks, with the new version I get some more hints. It seems that there is a problem with the path. Just having weblogo installed in the dependency directory and using the env.sh mechanism to set the path, the wrapper doesn't find the executable at all: ---%--- ## rgWebLogo3.py error - cannot locate the weblogo binary weblogo on the current path ## Please ensure it is installed and working from http://code.google.com/p/weblogo ---%--- When I put a soft link to a directory which is in the galaxy user's static path, I get a different error: ---%--- Traceback (most recent call last): File /local/data/home/galaxy/galaxy-dist/tools/rgenetics/rgWebLogo3.py, line 156, in checks,s = w.run() File /local/data/home/galaxy/galaxy-dist/tools/rgenetics/rgWebLogo3.py, line 127, in run s = self.runCL() File /local/data/home/galaxy/galaxy-dist/tools/rgenetics/rgWebLogo3.py, line 47, in runCL print sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % cl TypeError: not enough arguments for format string ---%--- Line 47 seems to lack the variable for the return code, when changing the line to print sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % (cl, rval) I get the following message: ---%--- ## rgWebLogo3.py error - executing weblogo -F png -c auto -o /local/data/galaxy_files/000/dataset_304.dat -U bits -t Galaxy-Rgenetics Sequence Logo -f /local/data/galaxy_files/000/dataset_286.dat -s large returned error code 1 ## This may be a data problem or a tool dependency (weblogo) installation problem ## Please ensure weblogo is correctly installed and working on the command line -see http://code.google.com/p/weblogo ---%--- So it still seems to boil down to my local weblogo installation. Sourcing the respective env.sh and executing the above command line, I get a valid png though (again with the warning mentioned before): ---%--- galaxy@imbc1:~/tmp/1$ source ~/dependencies/weblogo/default/env.sh galaxy@imbc1:~/tmp/1$ weblogo -F png -c auto -o /local/data/galaxy_files/000/dataset_304.dat -U bits -t Galaxy-Rgenetics Sequence Logo -f /local/data/galaxy_files/000/dataset_286.dat -s large /home/galaxy/python/lib/python2.6/site-packages/CoreBio-0.5.0-py2.6.egg/corebio/seq_io/_nexus/__init__.py:19: DeprecationWarning: the sets module is deprecated import sets ---%--- Could this be related to the way galaxy is setting the paths dynamically using the env.sh file? Do I have to adjust python paths in there as well? Regards, Holger On Tue, Jul 5, 2011 at 5:49 PM, Holger Klein h.kl...@imb-mainz.de wrote: Hi Ross, thanks for taking care of this issue. On 07/05/2011 12:31 AM, Ross wrote: Is this error seen on Galaxy main or test? If so please share the history with me so I can see the input and reproduce what sounds like a wrapper error? Otherwise, if this is on a private instance, and if the tool has never produced output successfully, then this may be a dependency installation problem - eg you may need to ensure that the weblogo3 executable is available and working correctly on the path used by your execution nodes. To assure yourself that your data works with the tool, please try running it on main using the same data, and let me know what you see? in fact it's a private instance of galaxy, it's the latest version of galaxy-dist (hg summary: 5743:720455407d1c). The input data is fine, it's a clustalw alignment in fasta format which can be used by the weblogo module on galaxy main. Maybe some background info on the weblogo installation helps: it's located below the tool_dependency_dir as defined in universe_wsgi.ini in weblogo/3.0 (with default as a link to 3.0). It contains the file env.sh which sets the PATH: export PATH=/home/galaxy/dependencies/weblogo/3.0:$PATH Starting the weblogo executable with the galaxy virtualenv python seems to work (just tested --help), although it returns a warning
Re: [galaxy-user] Weblogo results empty
AFAIK, the requirements stuff is still work in progress? Yes, of course you're right - there has to be a better way - particularly where there are complex inter-dependencies like weblogo/python/corebio On Thu, Jul 7, 2011 at 10:41 PM, Holger Klein h.kl...@imb-mainz.de wrote: Hi Ross, On 07/07/2011 12:38 PM, Ross wrote: Holger, thanks for finding those errors - I'll take a look shortly. What's the 'dependency directory' ? I don't think the wrapper knows anything about it. it's defined in universe_wsgi.ini: # The directory containing tool dependencies tool_dependency_dir = /local/data/home/galaxy/dependencies We only recently installed galaxy locally, and Nate pointed me towards this way to handle external tool dependencies. This issue here is related: https://bitbucket.org/galaxy/galaxy-central/issue/82/fix-the-tag-set-in-the-tool-configs Until now when tools didn't work with that mechanism (CCAT, clustalw) I simply put a link into a directory which is in galaxy's path. The tool assumes that the weblogo script is on the path when the actual job starts executing - wherever that is. If the weblogo script produces output it must be on the path after you source that script and working I think. So, the environment on the execution node must include the relevant path. Otherwise it won't work. What path does the execution host get when a galaxy job is run? Does it include the right path to that weblogo script (marked executable)? Can the user each job runs as execute it? I got a step further. The above mentioned mechanism with putting a link to the weblogo executable simply into the path didn't work, because the weblogo script uses the system-wide python (from #!/usr/bin/env python) which doesn't have the corebio module installed. When changing the interpreter to #!/home/galaxy/python/bin/python (galaxy-specific virtualenv) it works. Somehow I just assumed that with setting the PYTHON variable in the startup script would be sufficient. So, now it works, but I wonder if there's a mechanism that is cleaner than hard-coding the python interpreter? Is there a way to tell galaxy or wrapper scripts to use a specific python version? Regards, Holger On Thu, Jul 7, 2011 at 7:56 PM, Holger Klein h.kl...@imb-mainz.de wrote: Hi Ross, On 07/07/2011 02:07 AM, Ross wrote: Please try the new version 0.4 of the weblogo wrapper in galaxy-central #5772 - it has additional error reporting that may help clarify dependency or other problems and let me know how you go? thanks, with the new version I get some more hints. It seems that there is a problem with the path. Just having weblogo installed in the dependency directory and using the env.sh mechanism to set the path, the wrapper doesn't find the executable at all: ---%--- ## rgWebLogo3.py error - cannot locate the weblogo binary weblogo on the current path ## Please ensure it is installed and working from http://code.google.com/p/weblogo ---%--- When I put a soft link to a directory which is in the galaxy user's static path, I get a different error: ---%--- Traceback (most recent call last): File /local/data/home/galaxy/galaxy-dist/tools/rgenetics/rgWebLogo3.py, line 156, in checks,s = w.run() File /local/data/home/galaxy/galaxy-dist/tools/rgenetics/rgWebLogo3.py, line 127, in run s = self.runCL() File /local/data/home/galaxy/galaxy-dist/tools/rgenetics/rgWebLogo3.py, line 47, in runCL print sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % cl TypeError: not enough arguments for format string ---%--- Line 47 seems to lack the variable for the return code, when changing the line to print sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % (cl, rval) I get the following message: ---%--- ## rgWebLogo3.py error - executing weblogo -F png -c auto -o /local/data/galaxy_files/000/dataset_304.dat -U bits -t Galaxy-Rgenetics Sequence Logo -f /local/data/galaxy_files/000/dataset_286.dat -s large returned error code 1 ## This may be a data problem or a tool dependency (weblogo) installation problem ## Please ensure weblogo is correctly installed and working on the command line -see http://code.google.com/p/weblogo ---%--- So it still seems to boil down to my local weblogo installation. Sourcing the respective env.sh and executing the above command line, I get a valid png though (again with the warning mentioned before): ---%--- galaxy@imbc1:~/tmp/1$ source ~/dependencies/weblogo/default/env.sh galaxy@imbc1:~/tmp/1$ weblogo -F png -c auto -o /local/data/galaxy_files/000/dataset_304.dat -U bits -t Galaxy-Rgenetics Sequence Logo -f /local/data/galaxy_files/000/dataset_286.dat -s large /home/galaxy/python/lib/python2.6/site-packages/CoreBio-0.5.0-py2.6.egg/corebio/seq_io/_nexus/__init__.py:19: DeprecationWarning: the sets module is deprecated import sets ---%--- Could this be related
Re: [galaxy-user] Weblogo results empty
Thanks for your input and patience, Holger! Please try the new version 0.4 of the weblogo wrapper in galaxy-central #5772 - it has additional error reporting that may help clarify dependency or other problems and let me know how you go? On Tue, Jul 5, 2011 at 5:49 PM, Holger Klein h.kl...@imb-mainz.de wrote: Hi Ross, thanks for taking care of this issue. On 07/05/2011 12:31 AM, Ross wrote: Is this error seen on Galaxy main or test? If so please share the history with me so I can see the input and reproduce what sounds like a wrapper error? Otherwise, if this is on a private instance, and if the tool has never produced output successfully, then this may be a dependency installation problem - eg you may need to ensure that the weblogo3 executable is available and working correctly on the path used by your execution nodes. To assure yourself that your data works with the tool, please try running it on main using the same data, and let me know what you see? in fact it's a private instance of galaxy, it's the latest version of galaxy-dist (hg summary: 5743:720455407d1c). The input data is fine, it's a clustalw alignment in fasta format which can be used by the weblogo module on galaxy main. Maybe some background info on the weblogo installation helps: it's located below the tool_dependency_dir as defined in universe_wsgi.ini in weblogo/3.0 (with default as a link to 3.0). It contains the file env.sh which sets the PATH: export PATH=/home/galaxy/dependencies/weblogo/3.0:$PATH Starting the weblogo executable with the galaxy virtualenv python seems to work (just tested --help), although it returns a warning: ~/python/bin/python ./weblogo --help/home/galaxy/python/lib/python2.6/site-packages/CoreBio-0.5.0-py2.6.egg/corebio/seq_io/_nexus/__init__.py:19: DeprecationWarning: the sets module is deprecated import sets I also tested putting a link to the weblogo executable in the PATH that's defined for the galaxy user (as opposed to the dependency dir mechanism, that I have to admit I don't fully understand yet), but that also doesn't work. Could this be an issue of PYTHONPATH needing to be adjusted? Regards, Holger Thanks again. On Tue, Jul 5, 2011 at 12:34 AM, Holger Klein h.kl...@imb-mainz.de wrote: Dear all, I have a problem with the weblogo tool. I have a clustalw alignment in fasta format that I'd like to visualize as a logo. The sequence logo module ends with a success (green box), the info tells me the amount and length of the input data. But the output is empty, there are no plots (no matter if I select jpg, png, pdf or text). The respective image can't be displayed because it contains errors or is empty in case of text. I suspect that the actual call of the weblogo tool doesn't succeed, but I didn't figure out yet on how to check this. Does anybody have hints on where to look? Cheers, Holger ___ 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/
Re: [galaxy-user] Fastq uploads
Keith, TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator). is written on the screen right below the files box for this very reason. On Sat, Jun 11, 2011 at 6:50 PM, Keith Giles keithegi...@gmail.com wrote: I converted 2 fastq datasets, roughly 3 gb in size each. They have been queued up for about 24 hours now. Are they too big? What is the best way to upload large fastq datasets? Sent from my iPhone ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics
On Thu, Jun 9, 2011 at 10:12 AM, John David Osborne ozb...@uab.edu wrote:
Thanks Ross, I don't see it under my local install - are there any
pre-written scripts to integrate it with a local galaxy instance?
I assume you are talking about this tool here:
http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
Hi, John.
it's on main and test - ie the FastQC wrapper is distributed with the
current stable and central branches so your local tool_conf.xml may be
out of date since it's not automagically refreshed from the distro
.sample ? If you do a diff of your local tool_conf.xml with the
current distributed sample, you should see the lines you need to add
which points to rgenetics/fastqc.xml
Thu,Jun 09 at 10:22am grep -i fastqc tool_conf.xml
label text=FastQC: fastq/sam/bam id=fastqcsambam /
tool file=rgenetics/rgFastQC.xml /
Like everything else, you'll want to install the jar locally so it can
be found by the cluster - the default location is
tool-data/shared/jars/FastQC so the tool can find the fastqc perl
script (yes, I know...but it's worth it!)
command interpreter=python
rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file
-n $out_prefix -f $input_file.ext -e
${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc
I hope this helps?
-John
From: Ross [ross.laza...@gmail.com]
Sent: Wednesday, June 01, 2011 11:41 AM
To: John David Osborne
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics
You can avoid the space/time overhead of grooming and get
comprehensive QC reports using the new wrapper for FastQC (under NGS:
QC) - it takes fastq of any flavour (and bam) groomed or not,
producing a superset of the compute quality stats output without the
need for an intermediate step. Highly recommended.
On Wed, Jun 1, 2011 at 12:02 PM, John David Osborne ozb...@uab.edu wrote:
I noticed that for our new Ilumina data (which generate Sanger format) the
FastQ groomer output is identical to the Ilumina FastQ input file.
I was hoping to go ahead and just use the raw FastQ files as input (saving
disk space) for computing quality statistics to look at box plots, but it
appears that the tool Compute Quality Statistics appears to require that
the data have been run through FastQ Groomer first.
Is there a way to get around this and is this a bug? I assuming this is some
sort of safety measure built into this tool?
-John
___
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/
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
___
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/
Re: [galaxy-user] FastQ Groomer and Compute Quality Statistics
You can avoid the space/time overhead of grooming and get comprehensive QC reports using the new wrapper for FastQC (under NGS: QC) - it takes fastq of any flavour (and bam) groomed or not, producing a superset of the compute quality stats output without the need for an intermediate step. Highly recommended. On Wed, Jun 1, 2011 at 12:02 PM, John David Osborne ozb...@uab.edu wrote: I noticed that for our new Ilumina data (which generate Sanger format) the FastQ groomer output is identical to the Ilumina FastQ input file. I was hoping to go ahead and just use the raw FastQ files as input (saving disk space) for computing quality statistics to look at box plots, but it appears that the tool Compute Quality Statistics appears to require that the data have been run through FastQ Groomer first. Is there a way to get around this and is this a bug? I assuming this is some sort of safety measure built into this tool? -John ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
