Re: [galaxy-user] Text Manipulation
Hi Peter, sounds nice, would be a great feature. For everyone else how is not using a custom server: if you are lucky you can use the trim tool on tabs to solve your problem. If you want to add text to the beginning or end of a column: - Use add column and add the text as a new column - Then use cut to get everything in the right order - finally join the new column with the column you want to add the text to I hope you get what I mean and is helpful to someone Using these tricks I have created a work flow that serves as my custom sam to gff converter. Of course its terribly inefficient, but it gets the job done. thx, Felix On Tue, Feb 22, 2011 at 2:28 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Felix, Text Manipulation - Convert delimiters to TAB could split one field into more than one, but the delimiter has to be in the list (@ is not). Text Manipulation - Cut columns from a table is similar, but it will not split on a @ either. Text Manipulation - Trim leading or trailing characters could be use for this specific case, since you can trim off the end of a column based on a position (but again, not a specified delimiter). To prep for an entire genome, you would need to break up the starting query so that the chromosome name lengths in any derivative queries are of a consistent length, then merge back together. Perhaps the @ was just an example and one of these tools will work for you. If you are customizing, additions to the Tool Shed that expand the native tools are always welcome! http://community.g2.bx.psu.edu I've been planning to write a Galaxy tool to split a column on a given delimiter (e.g. @ for this example, or | for NCBI style identifiers), which would solve this use case nicely. I haven't done it yet though - so if anyone else wants to write such a tool first, please go ahead. Specifically I would be aiming to expose the Python split and rsplit string method functionality, so the user would have to specify the number of splits (or perhaps more intuitively the number of columns to make) and if it should start on the left (default) or on the 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. 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] Group and hide steps in history/workflow
Hi, it would be really nice if I could take a work flow and save it as a tool. This way one could easily build custom text-manipulation tools from already existing text tools. I already have a work flow that does a conversion job. But it has lots of of steps that make my histories quite messy when I apply it. Is there a way to condense the steps in the history view, so you can only see the name of a work flow and not all the separate steps? thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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] Group and hide steps in history/workflow
On Tue, Feb 22, 2011 at 1:23 PM, Felix Hammer hamm...@cip.ifi.lmu.de wrote: I've done that. The intermediate outputs are hidden. But all the steps are still displayed. I want to hide those, too. Felix I'm unclear which bit(s) you want to hide in the GUI. With the recent enhancements, the run workflow dialogue where you choose any options to the workflow, although still shown any step not taking options is now collapsed by default. This makes things much nicer as an end user. I do like the idea of treating a multi-step workflow as a single tool though... this would be especially helpful for connecting workflows together - one way to tackle this feature request: https://bitbucket.org/galaxy/galaxy-central/issue/52/subworkflows Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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] get wig file after tophat
HI, The option you need in IGV tools is count. You set a window size and this gives you a tdf file from your sorted bam (or sam) file which is nice and quick to view on IGV. Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 22 Feb 2011, at 15:52, Ying Zhang wrote: Dear David: thank you very much for helping me! I have download the IGV and I do find the IGVtools, however, I am not sure which tool I should use for generate a tdf file, the tile function will generate a tdf file, but the input file format does not include bam or sam file, instead it need wig file. But I have no wig file to put in. So I am wondering whether you need to use other tool first. I really appreciate your help! Thank you very much! Best Ying Quoting David Matthews d.a.matth...@bristol.ac.uk: Hi, You can get an equivalent visualisation from the IGV viewer by the Broad Institute - its under IGV tools and generates a tdf file from bam or sam files. This also gives a quick and easy way of looking at depth at any particular site and is very accessible. Cheers David On 21 Feb 2011, at 21:44, Jeremy Goecks wrote: Hi all, Ann is correct - Tophat does not produce .wig files when run anymore. However, it's fairly easy to use Galaxy to make a wiggle-like coverage file from a BAM file: (a) run the pileup tool on your BAM to create a pileup file; (b) cut columns 1 and 4 to get your coverage file. A final note: it's often difficult to visualize coverage files because they're so large. You might be better off visualizing the BAM file and using the coverage file for statistics. Best, J. Hello, I think I know the answer (sort of) to this question. This may be because newer versions of tophat stopped running the wiggles program, which is still part of the tophat distribution and is the program that makes the coverage.wig file. A later version of tophat might bring this back, however - there's a note to this effect in the tophat python code. So if you can run wiggles, you can make the coverage.wig file on your own. A student here at UNC Charlotte (Adam Baxter) made a few changes to the wiggles source code that would allow you to use it with samtools to make a coverage.wig file from the accepted_hits.bam file that TopHat creates. If you (or anyone else) would like a copy, please email Adam, who is cc'ed on this email. We would be happy to help add it to Galaxy if this would be of interest to you or other Galaxy users. If there is any way we can be of assistance, please let us know! Very best wishes, Ann Loraine On 2/21/11 3:39 PM, Ying Zhang ying.zhang.yz...@yale.edu wrote: Hi: I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out that after the tophat analysis, we can not get the wig file from it anymore which is used to be able to. Do you have any idea of how to still be able to get the wig file after tophat analysis? Thanks a lot! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/ -- Ann Loraine Associate Professor Dept. of Bioinformatics and Genomics, UNCC North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 www.transvar.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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. 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
Re: [galaxy-user] 2011 Galaxy Community Conference, May 25-26, Lunteren, The Netherlands
Hello all, Just a reminder that the abstract submission deadline for the Galaxy Community Conference is next Monday, February 28. See http://galaxy.psu.edu/gcc2011/Abstracts.html for details. Cheers, Dave C. PS: And there is still space at the GMOD Meeting being held March 5-6 @ NESCent: http://gmod.org/wiki/March_2011_GMOD_Meeting On Tue, Feb 1, 2011 at 9:19 PM, Dave Clements clementsgal...@gmail.comwrote: Hello all, We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. *Link: http://galaxy.psu.edu/gcc2011/ * *Overview * This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: * Talks submitted by the Galaxy community * Integration of tools (including NGS analysis tools) and distributed job management * Deployment of Galaxy instances on local resources and on the Cloud * Management of large datasets with the Galaxy Library System * Using the Galaxy LIMS functionality at NGS sequencing facilities * Visualizing Data without leaving Galaxy * Performing reproducible research * Performing and sharing complex analyses with Workflows * An Introduction to Galaxy session, offered on May 24, for Galaxy newcomers. *Registration * The conference fee is €100 on or before April 24, and €120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the Intro to Galaxy session) is limited and is likely to fill up before the conference itself does. *Link: http://galaxy.psu.edu/gcc2011/Register.html ** Abstract Submission * Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. *Link: http://galaxy.psu.edu/gcc2011/Abstracts.html * *Sponsors * The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC). NBIC is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. *Links: http://www.nbic.nl/ and http://www.nsf.gov/ * We are looking forward to a great conference and hope to see you in the Netherlands! The Galaxy and NBIC Teams -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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] get wig file after tophat
Ying, You can create a coverage file from a BAM file using this workflow: http://main.g2.bx.psu.edu/u/jeremy/w/create-coverage-dataset-from-bam-dataset While this doesn't generate a proper wiggle file, it can be a useful file for statistical analysis. I and others have suggested ways to visualize a BAM file with coverage data in mind: Trackster, IGV, and IGB. Thanks, J. On Feb 22, 2011, at 11:04 AM, Ying Zhang wrote: Dear Jeremy: Thank you so much for helping me! Followed your instructions, I do get the pileup file, however, I am a little bit confused about how you generate the wig file. So you mean to cut out the column 1 and 4, and use the rest of them to generate the wig file or cut the columns 1 and 4 and past it to another file to generate the wig file? The reason I am asking is that it looks like column 1 is the information of chromosome, I am not sure whether I should cut it out. Also I found out that the pileup file is kind of big, so how you can cut the column 1 and 4? do you need to run a command? I am basically not an expert in computer, do you know whether there is an easy way to do this task in windows? THank u so much! Best Ying Quoting Jeremy Goecks jeremy.goe...@emory.edu: Hi all, Ann is correct - Tophat does not produce .wig files when run anymore. However, it's fairly easy to use Galaxy to make a wiggle-like coverage file from a BAM file: (a) run the pileup tool on your BAM to create a pileup file; (b) cut columns 1 and 4 to get your coverage file. A final note: it's often difficult to visualize coverage files because they're so large. You might be better off visualizing the BAM file and using the coverage file for statistics. Best, J. Hello, I think I know the answer (sort of) to this question. This may be because newer versions of tophat stopped running the wiggles program, which is still part of the tophat distribution and is the program that makes the coverage.wig file. A later version of tophat might bring this back, however - there's a note to this effect in the tophat python code. So if you can run wiggles, you can make the coverage.wig file on your own. A student here at UNC Charlotte (Adam Baxter) made a few changes to the wiggles source code that would allow you to use it with samtools to make a coverage.wig file from the accepted_hits.bam file that TopHat creates. If you (or anyone else) would like a copy, please email Adam, who is cc'ed on this email. We would be happy to help add it to Galaxy if this would be of interest to you or other Galaxy users. If there is any way we can be of assistance, please let us know! Very best wishes, Ann Loraine On 2/21/11 3:39 PM, Ying Zhang ying.zhang.yz...@yale.edu wrote: Hi: I am using tophat in galaxy to analyze my paired-end RNA-seq data and find out that after the tophat analysis, we can not get the wig file from it anymore which is used to be able to. Do you have any idea of how to still be able to get the wig file after tophat analysis? Thanks a lot! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/ -- Ann Loraine Associate Professor Dept. of Bioinformatics and Genomics, UNCC North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 www.transvar.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/ Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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
Re: [galaxy-user] Generating pileup for SNP analysis
Hello Christine, We have confirmed that the reads have Sanger qual format, not Illumina (as were originally run in your history) or Solexa (as some are at NCBI, from other SRA projects, but not this one). Please re-run the Fastq groomer with Sanger as the input type and all should run correctly. Thank you again for working with us to resolve the issue and for using Galaxy! Please let us know if we can help more or if the results after the re-run are not what you expect. Best, Jen Galaxy team On 2/11/11 7:20 AM, Christine Picard wrote: I am a new user to Galaxy, and I was hoping someone might be able to help with this small problem. I am using Drosophila resequencing data downloaded from the SRA and trying to look for SNPs that differentiate the two strains. I've gotten as far as generating the pileup for each strain, but my column which has the consensus base is always an N. Can anyone help me out? thanks, Christine -- Christine J. Picard, Ph.D. Postdoctoral Research Associate Department of Entomology Texas AM University TAMU 2475 College Station, TX 77843-2475 christine.pic...@gmail.com mailto:christine.pic...@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. 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/ -- Jennifer Jackson http://usegalaxy.org 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. 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] fastx_clipper.xml and FASTQ Illumina 1.3+?
Hi Peter, For now we are going to recommended just using the Fastq Groomer first, then the Clipper, to keep the tools set simple. Apologies for the late reply, we were discussing the option internally. Thanks for all the great ideas and contributions! Best, Jen Galaxy team On 1/6/11 4:28 AM, Peter wrote: Hi all, Should the fastx_clipper.xml allow Illumina 1.3+ FASTQ as well as Sanger and Solexa FASTQ (and FASTA)? i.e. replace this: param format=fasta,fastqsolexa,fastqsanger name=input type=data label=Library to clip / with this: param format=fasta,fastqsolexa,fastqillumina,fastqsanger name=input type=data label=Library to clip / Peter ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org 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. 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] [galaxy-dev] Peep view for history elements broken on IE?
Hi Peter,
The error when clicking tool menu links is now fixed on galaxy-central tip.
Thanks for reporting!
On Mon, Feb 21, 2011 at 4:48 AM, Peter pe...@maubp.freeserve.co.uk wrote:
On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li kan...@gmail.com wrote:
All:
I retested under IE7 and found the bugs you were mentioning. This has
all
been fixed on trunk by using a newer local storage library. The only IE7
issue that I am now aware of is when the tool pane is empty when using
workflows. Please let me know if you see any other issues.
Thanks,
K
On Fri, Feb 18, 2011 at 10:50 PM, Kanwei Li kan...@gmail.com wrote:
The empty tool pane issue for IE is now fixed on tip as well.
Thanks,
-K
Hi Kanwei,
I presume this was the fix for the peep view not working on IE7,
https://bitbucket.org/galaxy/galaxy-central/changeset/1dfad17e81a8
That doesn't seem to have been included in the latest galaxy-dist
release.
I've tried both main.g2.bx.psu.edu and test.g2.bx.psu.edu with
IE7 and the peep view is still unchanged. Should the test machine
be working? Perhaps there is a caching problem...
Also, when using either main.g2.bx.psu.edu or test.g2.bx.psu.edu
with IE7 I am now getting a JavaScript error when I click on any tool:
Line: 52
Error: Object doesn't support this property or method
Offending line:
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
Context:
// Log clicks on tools.
$(div.toolTitle a).click( function()
{
var tool_title = $(this).attr('id').split(-)[1];
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
var search_active =
$(this).parents(div.toolTitle).hasClass(search_match);
// Log action.
galaxy_async.log_user_action(tool_menu_click. + tool_title,
section_title,
JSON.stringify({search_active : search_active}));
});
This may be unrelated, but you said you'd been working on the tool
pane too, so I'm mentioning it here rather than starting a new thread
or filing a bug..
Peter
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The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. For discussion of local Galaxy
instances and the Galaxy source code, please use the
Galaxy Development list:
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To manage your subscriptions to this and other
Galaxy lists, please use the interface at:
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[galaxy-user] Fwd: normalizing for number of tags
Hi Nadege, I am forwarding your question to galaxy-u...@bx.psu.edu which is the best place to send data questions, so that the entire team can provide input. We will get back to you as soon as possible. Thanks! Jen Galaxy team --- Hi Jen, I am completely new to the field of ChIP-seq and have, what may seem to many, a very trivial problem. Assuming that I have 2 datasets that I want to compare after normalizing each to their respective inputs, and assuming that these 2 datasets have very different number of reads to start with, how can I first normalize each dataset for number of reads in Galaxy? is it something that users do? Thanks for your precious help, best Nadege ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/
