Re: [galaxy-user] [blast-help] When will megablast be working again
Hi Scott, Could you clarify *which* Galaxy server you are using, and *which* megablast tool within Galaxy? Most BLAST options within Galaxy do NOT send the queries to the NCBI servers. (1) Main Public Galaxy I would guess you are using the main Galaxy Server, which only has this megablast wrapper using BLAST+ blastn internally for a limited set of databases (I would check but https://usegalaxy.org/ is down right now for me): galaxy-central/tools/metag_tools/megablast_wrapper.xml tool id=megablast_wrapper name=Megablast version=1.2.0 ... Current Galaxy stable source link: https://bitbucket.org/galaxy/galaxy-dist/src/3b3365a391944f848b403412f226ee9e5499c0d5/tools/metag_tools/megablast_wrapper.xml?at=default (2) A local Galaxy with the BLAST+ wrappers The BLAST+ wrappers that I manage all run BLAST on the local server/cluster, although we are looking at an option to run this via the NCBI using the -remote switch: https://github.com/peterjc/galaxy_blast/issues/39 (3) A local Galaxy with custom BLAST tools Are you perhaps using JJ's experimental BLAST+ wrappers with -remote support developed as part of the Galaxy-P project? See links on https://github.com/peterjc/galaxy_blast/issues/39 Thanks, Peter On Mon, Apr 28, 2014 at 5:25 PM, Scott W. Tighe scott.ti...@uvm.edu wrote: Dear Wayne Here is the error message I get back. Server Error Your request could not be processed due to a problem on our Web server. This could be a transient problem, please try the query again. If it doesn't clear up within a reasonable period of time, e-mail a short description of your query and the diagnostic information shown below to: pub...@nlm.nih.gov - for problems with PubMed webad...@ncbi.nlm.nih.gov - for problems with other services Thank you for your assistance. We will try to fix the problem as soon as possible. Diagnostic Information: Error: 500 URL: h t t p : / / b l a s t . n c b i . n l m . n i h . g o v / b l a s t / B l a s t . c g i ? Client: 130.14.26.12 Server: blast339 Time: Mon Apr 28 12:23:50 EDT 2014 NOTE: The above is an internal URL which may differ from the one you used to address the page. Rev. 01/04/08 -- Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999- (cell) Quoting Matten, Wayne (NIH/NLM) [C] mat...@ncbi.nlm.nih.gov: Hello, Scott, The web blast service, including megablast, is functioning normally. I don't know how Galaxy submits searches to us, but my guess is via our blast URLAPI, which is also functioning well at the moment. If your searches using our web page directly are also not working, please send me an RID from a search today, or describe a search in enough detail that I can reproduce it. Best regards, Wayne Wayne Matten, PhD NCBI Public Services mat...@ncbi.nlm.nih.gov On 4/28/14 9:56 AM, Scott W. Tighe scott.ti...@uvm.edu wrote: Dear NCBI and Galaxy Team I have sent a note to determine when the Megablast option will be active again. Whether you use Galaxy or NCBI directly, it is inoperative. Scott -- Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999- (cell) ___ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] [blast-help] When will megablast be working again
On Mon, Apr 28, 2014 at 9:01 PM, Scott Tighe scott.ti...@uvm.edu wrote: Peter Thank you for your detailed response and I should have noted that I was using the Main Public Galaxy. Thank you for confirming that it is down! I appreciate your input! Scott Hi Scott, Galaxy is back for me now, and yes, the Galaxy tool you are talking about is called Megablast (version 1.2.0), and only offers these target databases: htgs 13-Apr-2014 nt 17-Apr-2014 wgs 20-Apr-2014 phiX174 This Galaxy tool does *not* connect to the NCBI BLAST service over the internet. It sounds like the problem was due to the Galaxy team updating these databases - as Jennifer mentioned? I don't understand how you got an NCBI web server error message (in your email to Wayne), but perhaps you were separately testing the NCBI BLAST service outside of Galaxy? Regards, Peter ___ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] BioStar integration - merging accounts
Hi all, I see that https://biostar.usegalaxy.org is live now, with lots of content mined from the galaxy-user mailing list (which may or may not result in this email starting a new question? We shall see...). Is it possible for an admin to merge accounts? e.g. there are all me: https://biostar.usegalaxy.org/u/333/ - old ISP based email address https://biostar.usegalaxy.org/u/337/ - old ISP based email address https://biostar.usegalaxy.org/u/394/ - my Google mail address Thanks, Peter ___ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] BioStar integration - merging accounts
On Thu, Apr 24, 2014 at 2:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I see that https://biostar.usegalaxy.org is live now, with lots of content mined from the galaxy-user mailing list (which may or may not result in this email starting a new question? We shall see...). Is it possible for an admin to merge accounts? e.g. there are all me: https://biostar.usegalaxy.org/u/333/ - old ISP based email address https://biostar.usegalaxy.org/u/337/ - old ISP based email address https://biostar.usegalaxy.org/u/394/ - my Google mail address Thanks, Peter In answer to my own question, apparently accounts cannot be merged: https://biostar.galaxyproject.org/p/7287/ This surprises me as on BioStars administrators could merge accounts. Peter ___ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Unsubscribe
On Fri, Mar 14, 2014 at 9:58 AM, Elvio Pederzolli epede...@bigpond.net.au wrote: Hi there can you please unsubscribe me from all Galaxy lists please Thank you Elvio Pederzolli You should be able to unsubscribe yourself here: http://lists.bx.psu.edu/listinfo/galaxy-user Regards, 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/
Re: [galaxy-user] Galaxy + user program unable to locate files
On Thu, Feb 27, 2014 at 9:32 AM, do kadya doka...@gmail.com wrote: Hi, Thank You for your kind reply. I am having problem in running command in Galaxy. my current command: tool_name file_having_multiple_file_name_tab_delimited.txt or .tab file1.bam file2.bam /usr/bin/x_tool fileList.tab file1.bam file2.bam I have created xml file so that i can run this command through Galaxy. Its showing error: Can't call method print on an undefined value at /usr/local/share/perl/5.14.2/GTF/tool_x/Calc.pm line 110. When I am running same command from terminal, its working. From these I have hypothesize: - Galaxy is having different path to run its script, and different file name. - FileList.tab contains list of other files which present in same folder. - As tool is not able to search those files, may be galaxy is having different path where it run the command. --- While uploading file, I am using user defined path so that galaxy will not create replica of it, hence when I see error file of Galaxy output (by clicking on (i) symbol ) its showing the same path where all my files are located. Normally tool development questions are on the galaxy-dev list (CC'd). It sounds like your problem is inside your own Perl script? Perhaps within Galaxy there is a problem with the Perl environment variables defining where to find Perl libraries... 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/
Re: [galaxy-user] Galaxy + user program unable to locate files
On Thu, Feb 27, 2014 at 4:20 PM, do kadya doka...@gmail.com wrote: I don't think so that problem is in tool, because when I run same tool of normal terminal, it generate output. This is why I was asking about Perl environment variables - they may be different compared to when you run the tool. For example, is Galaxy run as a different Linux user? 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/
Re: [galaxy-user] special character $ gets converted to X in tool
On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi, In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable. Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI. Thanks, Ketan This is a security feature I think - or it may just need escaping as \$ Since you are writing the script, why not pass in the environment variable name without the dollar? 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/
Re: [galaxy-user] usegalaxy.org is down?
On Mon, Jan 20, 2014 at 3:53 PM, Leontovich, Alexey A., Ph.D. leontovich.ale...@mayo.edu wrote: Hello, It seems that usegalaxy.org is down. Is it? Thank you. Alexey Leontovich It was down yes, but should be OK now: @GalaxyProject on Twitter recently: After a short downtime we are back up and running! #usegalaxy https://twitter.com/galaxyproject/status/425314813946773504 However, it still seems to be a bit slow to load for me... 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/
Re: [galaxy-user] fastqc and blast? trinity?
On Sat, Dec 14, 2013 at 8:52 AM, Jorge Braun braun_...@hotmail.com wrote: Hello, of course, Jennifer is right for the first question . For the second question about blast ... I wonder if running after blast in galaxy I can remove sequences that can contaminate the data. It's possible? The BLAST suite is not available on the public Galaxy server at http://usegalaxy.org but is available from the Galaxy Tool Shed if you have a local Galaxy instance: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ One way to filter your FASTA file based on BLAST hits would be to use the tabular output from BLAST with this sequence filtering tool: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id e.g. If you want to remove transcripts which seem to be mitochondria, you could BLAST against a mitochondrial database, and take only the sequence with no hits. Regards, 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/
Re: [galaxy-user] help for trim sequences
On Fri, Nov 22, 2013 at 8:48 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Seung Hee, I know we discussed this on the other list, but I didn't point you to the open development ticket to (potentially) extend the functions of the Cut tool. This is not being actively worked on right now, but you can follow it for updates if you want. https://trello.com/c/CbFSHrU5 Others are still welcome to comment about what types of solutions they might have to offer. There is no specific tool to do this on Main right now (or in the Tool Shed, from my checks). http://usegalaxy.org/toolshed This tool of mine might do what Seung Hee wanted, but I have not tried it on very large Illumina datasets: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip Regards, 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/
Re: [galaxy-user] generating pileup with max depth greater than 8000?
On Wed, Sep 25, 2013 at 7:27 PM, Lauren Oldfield lm...@pitt.edu wrote: My question: How can I generate a pileup with an output of more than 8000 hits per base? I was generating pileups using the SAM tools -- Generate pileup and do not see an option to change the settings for output. In mpileup there is a variable that looks correct, -D (Output per-sample read depth) , but I cannot figure out how to adjust it. I checked the box, Output per-sample read depth, under the advanced settings but the log file generated still says the max depth was 8000. The pileup files I generated look great but I would like to know what the true read depth is at the 8000 hit plateaus. Hi Lauren, Unfortunately this is a samtools design choice, 8000 is the coverage limit hard coded in the source code itself (see files bam_pileup.c and bam_plcmd.c), so at the very minimum it would mean manually editing the samtools source and recompiling samtools. It would be best to ask about this on the samtools-help mailing list (CC'd), as it may be more complicated than just editing a few lines of the C code. For the samtools folk - could this magic limit of 8000 be done via a #define to make it clearer this is a special constant, and give people just one place to change the code? Any help appreciated. I'm a little out of my depth here. Ha ha, good pun. 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/
Re: [galaxy-user] watching command line to a query
On Tue, Aug 27, 2013 at 2:07 PM, lilach noy lilach...@gmail.com wrote: Thank you for the reply. Where can i find the log file? As an ordinary Galaxy user, I'm not sure if this is possible. You would have to be running your own Galaxy instance, look at the file paster.log in the main Galaxy folder. 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/
Re: [galaxy-user] tool within a tool
On Thu, Aug 22, 2013 at 12:07 AM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi, I am wondering if it is possible in Galaxy to design a tool whose sole purpose is to run other tools. This is motivated by our desire to enhance execution capabilities of existing tools via a generic tool which acts as a wrapper. This sounds a bit like the idea of making a workflow into a tool (or act in a tool like manor)... but I think you'd be better off raising this question on the Galaxy Development list: http://lists.bx.psu.edu/pipermail/galaxy-dev/ 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/
Re: [galaxy-user] Bowtie: Outputting unmapped reads
On Wednesday, July 31, 2013, Mayank Tandon wrote: That's a neat trick, and I definitely wouldn't have thought of that approach, so thanks for that! After I finished writing this out, I realized it was super long. So here are the questions I'm asking up front, so you can choose whether or not to read the details. Thanks! 1. How do I output the quality scores when converting from FASTQ to FASTA? You can't, unless you mean converting a FASTQ file into a FASTA and matching QUAL file? 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/
Re: [galaxy-user] viewing data live while tool is running
On Tue, Jul 30, 2013 at 5:27 PM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi, I am a relatively new Galaxy user. I am wondering if there is an example of a tool which allows users to view at the stdout/err of a tool live while it is still running to get a sense of progress it is making. The tools I have had experience with so far will save the stdout/err or an elaborate report as they are running and those results would be available for users only after the tool has completed running. Admittedly I have not searched through the toolshed exhaustively. Best, -- Ketan I'm pretty sure Galaxy won't allow you to view any of stdout/stderr until the tool has finished - this is especially true if run on a cluster. However, if the tool's stdout is redirected to an output file shown in the Galaxy history you should be able to see that as the job runs. My MIRA wrapper does this, I have a Python wrapper script calling MIRA via subprocess and sending MIRA's stdout to a text file defined as one of the outputs in the Galaxy XML. http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler Note that from Galaxy's point of view it was calling my Python script which produced a small amount on stdout - which is not available until the job finishes. 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/
Re: [galaxy-user] Rename tool output file in Galaxy
On Wed, Jul 24, 2013 at 5:21 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: Hi group, The galaxy stores the output of the job on files/043/dataset_ID.dat. I have two questions here.: 1) Can I find the ID of my output from the Galaxy history? I tried Edit Attributes, Annotations, tags but couldn't find it. Via the i icon of a history entry (information) you can see the datafile's full path which includes the ID. 2) Can I rename my output while initiating the task? If I can how can I do this and what are the consequences. Yes, you can. Normally this is fine. (Note sure if there can be complications with meta-data normally added automatically by inspecting the finished file...) 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/
Re: [galaxy-user] Rename tool output file in Galaxy
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/
Re: [galaxy-user] Rename tool output file in Galaxy
On Wed, Jul 24, 2013 at 11:15 AM, 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. You *cannot* rename the file on disk (without bypassing Galaxy and editing the database and renaming the file directly). This is by design - unless you are an administrator debugging something or a tool author you don't need to know the actual filename on disk. You *can* rename the description of the file as shown within the Galaxy interface (via edit attributes). 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/
Re: [galaxy-user] Filter Fastq
On Thu, May 9, 2013 at 12:27 PM, Casey,Richard richard.ca...@colostate.edu wrote: Hi, We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run? Which FASTQ filtering tool exactly are you referring too? The one called Filter FASTQ reads by quality score and length in the left hand column, tool ID fastq_filter? How big were the input files? 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/
Re: [galaxy-user] GenBank database files
On Mon, Apr 29, 2013 at 3:27 AM, Mike Dyall-Smith mike.dyallsm...@gmail.com wrote: Dear Peter Cock, thanks for your advice. Just to be clear, do I leave the files within their decompressed folders or do I put all the individual files into one folder? I assume the former, but want to be sure. Thanks again, Mike DS Hi Mike, Unless you're using a Graphical decompression tool which is trying to be too helpful, each tar-ball does *not* decompress into its own folder. The files should all be in the *same* folder. I use this to verify the checksums, $ md5sum --check nr.00.tar.gz.md5 nr.00.tar.gz: OK Then I use this to decompress the tar-balls, $ tar -zxvf nr.00.tar.gz etc (Actually I don't do this personally any more - it has been setup to happen automatically when the NCBI update the databases.) We keep all our NCBI databases in the same folder, $ ls /data/blastdb/ncbi/nr.* /data/blastdb/ncbi/nr.00.phd /data/blastdb/ncbi/nr.00.phi /data/blastdb/ncbi/nr.00.phr /data/blastdb/ncbi/nr.00.pin /data/blastdb/ncbi/nr.00.pnd /data/blastdb/ncbi/nr.00.pni /data/blastdb/ncbi/nr.00.pog /data/blastdb/ncbi/nr.00.ppd /data/blastdb/ncbi/nr.00.ppi /data/blastdb/ncbi/nr.00.psd /data/blastdb/ncbi/nr.00.psi /data/blastdb/ncbi/nr.00.psq /data/blastdb/ncbi/nr.00.tar.gz /data/blastdb/ncbi/nr.00.tar.gz.md5 ... /data/blastdb/ncbi/nr.10.phd /data/blastdb/ncbi/nr.10.phi /data/blastdb/ncbi/nr.10.phr /data/blastdb/ncbi/nr.10.pin /data/blastdb/ncbi/nr.10.pnd /data/blastdb/ncbi/nr.10.pni /data/blastdb/ncbi/nr.10.pog /data/blastdb/ncbi/nr.10.ppd /data/blastdb/ncbi/nr.10.ppi /data/blastdb/ncbi/nr.10.psd /data/blastdb/ncbi/nr.10.psi /data/blastdb/ncbi/nr.10.psq /data/blastdb/ncbi/nr.10.tar.gz /data/blastdb/ncbi/nr.10.tar.gz.md5 /data/blastdb/ncbi/nr.pal We can then refer to the NR database at the command line as /data/blastdb/ncbi/nr or as just nr if the BLAST database path is configured to check this folder. In this folder we also have other NCBI database, like NT: $ ls /data/blastdb/ncbi/nt.* /data/blastdb/ncbi/nt.00.nhd /data/blastdb/ncbi/nt.00.nhi /data/blastdb/ncbi/nt.00.nhr /data/blastdb/ncbi/nt.00.nin /data/blastdb/ncbi/nt.00.nnd /data/blastdb/ncbi/nt.00.nni /data/blastdb/ncbi/nt.00.nog /data/blastdb/ncbi/nt.00.nsd /data/blastdb/ncbi/nt.00.nsi /data/blastdb/ncbi/nt.00.nsq /data/blastdb/ncbi/nt.00.tar.gz /data/blastdb/ncbi/nt.00.tar.gz.md5 ... /data/blastdb/ncbi/nt.13.nhd /data/blastdb/ncbi/nt.13.nhi /data/blastdb/ncbi/nt.13.nhr /data/blastdb/ncbi/nt.13.nin /data/blastdb/ncbi/nt.13.nnd /data/blastdb/ncbi/nt.13.nni /data/blastdb/ncbi/nt.13.nog /data/blastdb/ncbi/nt.13.nsd /data/blastdb/ncbi/nt.13.nsi /data/blastdb/ncbi/nt.13.nsq /data/blastdb/ncbi/nt.13.tar.gz /data/blastdb/ncbi/nt.13.tar.gz.md5 /data/blastdb/ncbi/nt.nal Note you don't need to keep the *.tar.gz and the *.md5 files once you've verified the checksum (using md5sum to detect any data corruption during download) and decompressed the tar-ball. Peter P.S. This galaxy-users list is meant for discussion of using the tools within Galaxy from an end user perspective. Although there is talk about creating a new Galaxy mailing list specifically for deployment questions like this, currently galaxy-devel is preferred for this kind of discussion. ___ 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] GenBank database files
On Sun, Apr 28, 2013 at 11:22 PM, Mike Dyall-Smith mike.dyallsm...@gmail.com wrote: This should be easy (but not for me so far). I want to do local blast searches, so I download the premade nr protein blast database from GenBank. It is split into 10 .tar.gz files. I've decompressed them all, and now I want to put all the file parts together. Can I simply concatenate all similar files? (e.g. all 10 parts of the .phd files). The Readme mentions use of an alias file, but I did not find this at all clear. A set of step-by-step decompression and restoration instructions would be useful. I could not find any. Thanks for any assistance, Mike DS Don't cat anything - just download all nr.*.tar.gz files, and decompress them. You'll have a load of files including a special alias file called nr.pal which is how BLAST knows how to deal with the combined 'nr' database. 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/
Re: [galaxy-user] Change format with edit attributes
On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos ge2sa...@gmail.com wrote: Hello, I'm trying to change the format to the output files from Barcode splitter from FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read that it can be done through the edit attributes, I go to datatype and select fastaq, save and then go to convert format and press convert but the resulting file is 0 bytes and is not recognized by Bowtie. I´ve also tried to upload by copying the link and selecting fastaq as format but in this case, I got the file shown in the picture and it is not recognized by Bowtie again. What can I do?? I don´t know how to continue because I´m not able to change the format to fastaq! Thank you very much for your help in advance Best, Gema Hi Gema, There seem to be several factors confusing you here. The screenshot shows FASTA data wrongly labelled as FASTQ. The Galaxy edit attributes does NOT actually edit the data. There are separate tools which can convert from one format to another, which gives you a new entry in the history (another green box on the right). You can convert from FASTQ to FASTA, but doing the opposite is not possible without inventing quality scores (e.g. give everything score 30). Does that help? Peter Screen Shot 2013-04-03 at 4.37.50 PM.png___ 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] [galaxy-dev] History not updating for multiple instances of Galaxy
On Thursday, February 21, 2013, wrote: Further, when I try “register” I add an email address and password, but the system still doesn’t log me in ** ** Maybe this is a database configuration issue? ** ** I didn’t think I’d need to state any specific entries in universe as I am using physically separate directories ** ** i.e. /home/galaxy/galaxy-cte/ i.e. /home/galaxy/galaxy-Newcastle/ ** ** Cheers Neil The logging in problem sounds like a cookie path issue to me, I had something similar when I added second public Galaxy to our server (in my case, a live on and a dev one). 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/
Re: [galaxy-user] User's information
On Friday, November 30, 2012, Sachit Adhikari wrote: Where are the user's information stored in Galaxy? I can't find the information in universe_wsgi. Regards, Sachit It is in the database (PostgreSQL usually, but MySQL is also supported, and for simple test setups even SQLite mostly works). The users' files are all on disk (with the extension .dat regardless of the file type). 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/
Re: [galaxy-user] combining two fastq files
On Tue, Nov 27, 2012 at 9:51 PM, shamsher jagat kanwar...@gmail.com wrote: Is there an option in galaxy to combine two fastq files? Thanks kanwar Yes, but what do you mean by combine? Interleave? Concatenate? 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/
Re: [galaxy-user] Find out sense and antisense sequences
On Mon, Nov 26, 2012 at 6:47 PM, Zhiqiang Shu z...@bio.fsu.edu wrote: Hi, Galaxy users! I have a question on how to find out sense and antisense sequence. I've got RNA seq data in the fastq format. The sequences inside are partially complementary to each other (complementary is 10nt, while entire is about 30nt). How can I separate these sequences into two groups: sense and antisense Depending on how your sequences were prepared, you might be able to look for a poly-A tail as a clue to orientation. Another approach is to compare the (assembled) transcripts to known genes and if you only get matches on one strand that is probably the correct orientation. (one thing I know is for the sense sequence the 10th nucleotide is always A)? Why is that? Is this related to your library preparation? 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/
Re: [galaxy-user] stderr on Samtools sort
On Wed, Nov 14, 2012 at 9:00 AM, Masaki MS msmorioka-...@umin.ac.jp wrote: Dear all, I'm trying to set up samtools sort command on local Galaxy server. But I can not success to get sorted files from its result. I thought Galaxy tried to keep SAM/BAM files sorted by default... First time, I got error message from Galaxy as.. error at.. [bam_sort_core] merging from 13 files... To resolve this problem, I use discard_stderr_wrapper.sh for modifying my samtools_sort.xml. (http://wiki.galaxyproject.org/Future/Job%20Failure%20When%20stderr) That wiki is out of date now, and should point you to the stdio, regex, and exit_code tag sets documented here: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax Using these new features you can avoid a wrapper script just to hide stderr. 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/
Re: [galaxy-user] How to merge Fastq groomer files in Galaxy?
On Tue, Oct 16, 2012 at 8:22 PM, Fang,Xiefan xiefanf...@ufl.edu wrote: Dear Galaxy users, Does anyone know how to merge several FASTQ groomer files by using Galaxy? If not, is there any other program that can achieve this? The size of one FASTQ groomer file is around 1GB. Thank you! The Galaxy tool Concatenate datasets tail-to-head under Text Manipulation should work. I'm assuming you just need a simple concatenation of individual FASTQ files, not a more complex merge dealing with duplicates or sorting. 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/
Re: [galaxy-user] Cannot install ncbi_blast_plus or other tools from Tool Shed: HTTP 500 error
On Mon, Oct 8, 2012 at 8:26 AM, Joel Rosenberg thisisj...@hotmail.com wrote: So I'm trying to install the recently migrated ncbi_blast_plus tool from the Tool Shed to my local galaxy instance running in EC2 and am getting errors at the installation step. After clicking Install to local Galaxy I immediately get: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) and an HTTP 500 error code is returned. Chrome tells me the URL it's attempting to request is: http://toolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?changeset_revisions=a4b9836f8f47repository_ids=cd0d8ada19d98f27 Trying that URL in Firefox also gives the Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) message. It looks like a problem in the public ToolShed. Peter P.S. Problems with local Galaxy installs are normally discussed on the galaxy-dev list (CC'd) rather than galaxy-user list. ___ 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] blast tools on free public server
On Wed, Oct 3, 2012 at 3:54 PM, John DeFilippo defilippo.j...@gmail.com wrote: We're using the free public Galaxy server (main.g2.bx. psu.edu). We uploaded a genome FASTA sequence via ftp, and want to do BLAST searches (e.g., tblastn) against protein sequences that we've also uploaded to Galaxy, as well as on NCBI. BLAST tools don't show in the tools column, or when entered in the search box. Google searches on 'BLAST in Galaxy' bring up pages on 'wrappers' and xml, and we're but humble biologists. Can anyone please explain (simply, presuming no knowledge of wrappers, perl, python, java, scripts, xml, etc. on our part) how we can do this? Thank you. John D Offering BLAST searches is potentially quite computationally expensive, so for the moment at least the BLAST+ suite is not made available on the public Galaxy hosted by Penn State (with the exception of the megablast function offered with four databases only). The BLAST+ wrappers are available on the Galaxy Tool Shed, and can be installed to any local Galaxy server. They can then be run on your local server (and ideally your local cluster). That's what we do. If you have a Galaxy installation at your institute/department/... ask the local Galaxy administrator about this. Regards, 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/
Re: [galaxy-user] git mirror
On Tue, Sep 4, 2012 at 5:57 PM, Luca Pireddu pire...@crs4.it wrote: Hello list. A simple question: is there a git mirror of the Galaxy repositories? If not, what do git users here do to work with the Galaxy code base? Thanks, I don't think there is an official git mirror, but even if there was it wouldn't help for pushing changes or suggestion into Galaxy. Speaking as a git user who only has to use hg for Galaxy, I just learnt enough hg to get the basics done, and frequently consult resources like this: http://mercurial.selenic.com/wiki/GitConcepts#Command_equivalence_table 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/
Re: [galaxy-user] Installing Galaxy and Hooking into a SGE Cluster
On Thu, Aug 23, 2012 at 8:44 PM, mailing list margeem...@gmail.com wrote: Anyway, back to my question. Does anyone know? Would I be better off asking on the developer mailing list or perhaps Stack Overflow? Software licensing is a much broader issue that Galaxy, so yes, perhaps Stack Overflow would be a better place. 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/
Re: [galaxy-user] Aggregate collections of files (example: Heatmaps)
On Tue, Aug 21, 2012 at 4:46 PM, Ted Goldstein t...@soe.ucsc.edu wrote: I am developing several tools that will need to read and write multiple data files at once. For example, Eisen Cluster produces a heatmap which consists of three files: a .cdt file, .atr file and a gtr file which are the underlying heatmap and the array tree and the gene tree. All three files need to be kept together. I guess I could wrap them in a zip file and pack and unpack them.The heatmap is not just a view only object. Some tools, such as cuttree, would extract one tree and then aggregate genes (or arrays) below a certain depth and create a new trio of files. Is there support for (or plans for creating) any aggregate data types? Hi Ted, There is support for composite datatypes, so this should be possible. http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes This kind of discussion is normally directed to the galaxy-dev list (CC'd) 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/
Re: [galaxy-user] Help with Summary Statistics
On Thu, Aug 2, 2012 at 7:50 PM, D. A. Cowart dac...@psu.edu wrote: Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: That was probably FASTA format (but mangled in the email). I have attempted to use the Summary Statistics button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Use the Compute sequence length tool to compute the read lengths, and then you should be able to compute some statistics about the lengths. 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/
Re: [galaxy-user] Running Cufflinks on Bacterial RNAseq data
On Tue, Jul 31, 2012 at 7:35 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Rachel, When datasets are in a grey waiting to run state this indicates that they are in the queue and in line to run. For the majority of cases, including yours, leaving the job alone and allowing it to run is the correct option. The missing metadata only means that the result has not yet posted to your history (expected when still grey). It looks as if your jobs have now run, but resulted in errors. I can let you know that the problem is with the input GFF3 dataset. It contains at least one duplicated ID attribute, which is required to be unique within GFF3 files. Actually that isn't quite right (although it may be a limitation imposed by some tools using GFF3 as an input). Features split over multiple locations are described in GFF3 using multiple lines sharing the same ID attribute. This is most commonly used for genes made up of multiple exons, but can even apply across references in some extreme trans-splicing cases. 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/
Re: [galaxy-user] MegaBLAST output
On Tue, Apr 24, 2012 at 10:24 PM, Jennifer Jackson j...@bx.psu.edu wrote: ..., using the BLAST+ BLASTN megablast wrapper that Peter authored, in a local or cloud instance, would be the best immediate remedy (this version has the standard 12 column output). Sequence length data could always be obtained from Genbank and added into these results using other Galaxy tools (column join, etc.). Getting the query and match sequence lengths is even simpler that that with the BLAST+ wrappers - just select the extended tabular output. Of course, you'll need to adjust the downstream analysis to take into account the different column numbers. 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/
Re: [galaxy-user] Blast2GO local instance Re: Table with gene count reads
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: Have you seen the README file that comes with the Blast2GO wrapper? Perhaps the 'install from toolshed' could be tweaked to make this kind of documentation more visible... If you are installing a single repository that contains a file named one of (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of the file will be displayed on the tool panel section selection page. An example using the antismash repository on the main tool shed is below. This new feature is available in change set revision 6945:5ea04ccb61e8, which is currently running on the Galaxy tool shed and our central development repository. It will be available in the next Galaxy distribution. Great. In this case I've actually called the file blast2go.txt (to match the use of blast2go.xml and blast2go.py). I didn't want to use a generic name like README since there could be other tools installed in the same folder (this predates the auto-install system). Is this naming pattern common used enough to justify including in the Galaxy Tool Shed code for spotting a README file? Care must be taken when following instructions in README files since some of the information may be outdated. For example, the Galaxy functional test framework was recently enhanced to support testing tools included in installed repositories, but I've seen some README files currently in repositories that instruct installers to move test data to the Galaxy installation environment, which is no longer necessary. Some of my tools' README files will need a little clarification following those changes to Galaxy. Thanks, 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/
Re: [galaxy-user] Trouble with BLAST+ and .loc file
2012/3/21 Makis Ladoukakis makis4e...@hotmail.com: Dear Galaxy users, I have been trying to upload a blastable database in my local instance of galaxy. I have used the nr database and generated all the nhr, nin, nsq, and nal files. I have also edited the blastdb.loc file in the galaxy-dist/tool-data/ directory and it looks like this: database [build data] path nr_01_Mar_2012 nr 15 Mar 2012 /home/user/Desktop/nr.00/nr Nevertheless when i start galaxy the megablast tool can't recognise the database. Am I missing something? The NR database comes split up into many parts, 00 to 06 currently, and you need to download them all. They are linked by the nr.pal file, which you should also have downloaded. The database is then used via the full name of the nr.pal file (but without the .pal extension). If you are running Galaxy on a server, it is likely your systems administrator can/has setup a shared set of NCBI BLAST databases for all the system users (including Galaxy), to avoid unnecessary copies under /home Note that queries about local Galaxy installations are normally handled via the galaxy-dev mailing list (although perhaps the project needs three lists now given local Galaxy installations are getting more common and not everyone wants to follow the Galaxy development itself). 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/
Re: [galaxy-user] Trouble with BLAST+ and .loc file
On Wed, Mar 21, 2012 at 10:21 AM, Peter Cock p.j.a.c...@googlemail.com wrote: 2012/3/21 Makis Ladoukakis makis4e...@hotmail.com: Dear Galaxy users, I have been trying to upload a blastable database in my local instance of galaxy. I have used the nr database and generated all the nhr, nin, nsq, and nal files. I have also edited the blastdb.loc file in the galaxy-dist/tool-data/ directory and it looks like this: database [build data] path nr_01_Mar_2012 nr 15 Mar 2012 /home/user/Desktop/nr.00/nr Nevertheless when i start galaxy the megablast tool can't recognise the database. Am I missing something? The NR database comes split up into many parts, 00 to 06 currently, and you need to download them all. They are linked by the nr.pal file, which you should also have downloaded. The database is then used via the full name of the nr.pal file (but without the .pal extension). If you are running Galaxy on a server, it is likely your systems administrator can/has setup a shared set of NCBI BLAST databases for all the system users (including Galaxy), to avoid unnecessary copies under /home Note that queries about local Galaxy installations are normally handled via the galaxy-dev mailing list (although perhaps the project needs three lists now given local Galaxy installations are getting more common and not everyone wants to follow the Galaxy development itself). Peter Sorry, I missed something else which is vitally important: The NCBI NR database is a protein database, and should be listed in blastdb_p.loc (which is used by the BLASTP wrapper etc) while blastdb.loc is for nucleotide databases only (and used for the BLASTN/megablast wrapper etc). As you were asking about megablast, you probably want the NCBI NT BLAST database instead (although sometimes confusingly the NCBI can use the names ambiguously, for the file names this is very important). 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/
Re: [galaxy-user] Combining two workflows into one
You forgot to CC the mailin list. On Mon, Mar 19, 2012 at 12:02 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Mar 19, 2012 at 4:53 PM, Innocent Onsongo onson...@umn.edu wrote: Galaxy Team, I would like to create a workflow by combining portions of two different workflows. How do I do this in Galaxy? Thanks, Getiria Onsongo One outline solution is as follows: (1) Start with an empty history. (2) Upload/import the input files (3) Run first workflow (4) Run second workflow (5) Save history as a new combined workflow (6) Edit new workflow to remove any redundant steps This is of course limited in functionality compared to what might be possible in a future version of Galaxy. Peter On Mon, Mar 19, 2012 at 5:05 PM, Innocent Onsongo onson...@umn.edu wrote: I was hoping I could avoid re-running the two workflows since they both take a relatively long time to run. Looks like I might have to do it after all. Use smaller datasets? Ideally you would have a small test set covering positive and negative example. Or you can manually create the workflow in the workflow editor, starting from one of the existing ones and adding the new tools and connecting them together. 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/
Re: [galaxy-user] Metagenomics
On Mon, Mar 12, 2012 at 6:28 PM, John Major john.e.major...@gmail.com wrote: A small warning re-the current cloud-Blast+ config. To properly use the metagenomic tools, if you use the blast+ galaxy tool, make sure to export in blast.XML, then you'll need a script to parse out the readID and the Hit_def (as the hit ID). It appears that the 'Hit_def' field contains the correct key to the taxonomy database. Specifically, the Hit_def field is in the format #_#, where the 'gi' id is the first #. The tabular (normal and extended) data does not contain this info. I noticed this after attempting to use the tabular data, and using a trimmed col[1] (supposed to be hit seqID), but my results always came back as a ranked list of the most sequenced genomes in nt basically keying in randomly. j Hi John, Can you expand on that with a specific example (ideally on the galaxy-dev list, CC'd, since BLAST+ isn't event available on the public galaxy)? Also which version of BLAST+ are you using since I recall some changes to the tabular output IDs prior to 2.2.25 (which is what the wrappers were tested on, I've not tried 2.2.26 yet). Thanks, 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/
Re: [galaxy-user] Galaxy unable to set metadata for GFF files
On Sun, Mar 4, 2012 at 6:34 PM, Hemarajata, Peera hemar...@bcm.edu wrote: Dear all, I’m been trying to get Galaxy to recognize this GFF from NCBI ( ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Lactobacillus_reuteri_JCM_1112_uid58875/NC_010609.gff) but it failed to recognize the format after I uploaded it. That *could* be because the NCBI's GFF3 is still horrible broken, but they are working on it and the next release should have valid GFF which I am looking forward to. http://blastedbio.blogspot.com/2011/08/why-are-ncbi-gff3-files-still-broken.html However, if you get similar problems with a GFF3 file converted from GenBank using BioPerl, then I guess it is a Galaxy issue. 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/
Re: [galaxy-user] [galaxy-bugs] GI errors in the megablast table of results ?
Hello all, Did this issue get resolved? If Sandrine was right about there being an off by one error in GI number in the BLAST tabular output, it could be a bug in 'legacy' blastall command. I say 'legacy' BLAST because that's what Galay's NGS 'megablast' tool is using internally (as opposed to the the NCBI's replacement BLAST+). Peter On Wed, Jan 25, 2012 at 3:14 PM, Guru Ananda g...@psu.edu wrote: Dear Sandrine, Thanks for pointing out this issue. The BLAST databases we have on Galaxy are from last year, while those on NCBI website are the latest (Jan 2012). As pointed out on NCBI website (http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html), it appears that each time any change is made to a sequence/database, GI numbers change as well. This is perhaps why you're observing discrepancies in GI numbers and lengths between megablast outputs on Galaxy and NCBI. I'm currently in the process of downloading the latest BLAST databases from NCBI, and I'll let you know when they're available for use on Galaxy. Thanks for your patience, Guru Galaxy team. On Wed, Nov 9, 2011 at 8:03 AM, Sandrine Hughes sandrine.hug...@ens-lyon.fr wrote: Dear all, I’m not sure where I need to send my email so I apologize if I’m wrong. I have a trouble with the Megablast program available in NGS Mapping and I hope that you can help. Indeed, I think that there might be a problem with the table given in output, and notably a shift between the GI numbers and the parameters associated. Here are the details: I. First, what I have done : I used the program to identify the species that I have in a mix of sequences by using the following options: Database nt 27-Jun-2011 Word size 16 Identity 90.0 Cutoff 0.001 Filter out low complexity regions Yes I run the analyses twice and obtained exactly the same results (I used the online version of Galaxy, not a local one). II. Second, I analysed the data obtained for one of my sequence (1-202). The following lines are the beginning of the table that I obtained after the megablast and two lines with troubles: 1-202 312182292 484 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 312182201 476 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 308228725 928 99.33 150 1 0 1 150 19 168 2e-75 289.0 1-202 308228711 938 99.33 150 1 0 1 150 22 171 2e-75 289.0 1-202 308197083 459 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392378 920 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392376 918 99.33 150 1 0 1 150 9 158 2e-75 289.0 1-202 300392375 922 99.33 150 1 0 1 150 11 160 2e-75 289.0 1-202 300392374 931 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392373 909 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392371 1172 99.33 150 1 0 1 150 9 158 2e-75 289.0 ... 1-202 179366399 151762 98.67 150 2 0 1 150 46880 47029 6e-73 281.0 1-202 58617849 511 98.67 150 2 0 1 150 21 170 6e-73 281.0 III. Third, what I’ve noticed: My first trouble was that among all the species identified, two were very different from the expected ones (2 last lines). So I decided to search if that could be possible for that sequence and performed independently a megablast on the NCBI with similar options. I was not able to find these two species in the results. So, I decided to check the hits identified in the table above and identified a second trouble. In the table, the second column give the GI of the database hit and the third column give the length of the database hit. However, when I manually checked in NCBI the length of the GI, this one was incorrect. Indeed, for the GI 312182292, the length should be 580 and not 484. By checking different lines, I noticed that the length that is given for a GI corresponds to the length of the GI-1. As you can see in the above table, some GI are consecutive (300392376, 300392375,...). When checking the length of 300392376 in NCBI, I should have 920. But when I checked 300392375, I found 918. And this was true for the following lines : 300392374 give normally 922 and 300392373 give 931... My conclusion at that point was that there was a shift of –1 between the GI and the other parameters of the line (indeed the parameters for the remaining columns are in agreement with the
Re: [galaxy-user] wrapper question prefix for output files.
On Thu, Feb 23, 2012 at 5:46 PM, Victor Ruotti ruo...@wisc.edu wrote: Hi, I hope someone can help me on how to implement this into a wrapper. This kind of question is normally redirected to the galaxy-dev list. We would like to add an option so the user can set a sample name which then be used for the prefix of the output files names. You have no control over the file names at all - Galaxy will assign something like database/files/000/dataset_547.dat automatically. The user never sees the file names anyway. Are you asking about how to control the description/caption shown to the user in Galaxy? 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/
Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer
On Mon, Feb 13, 2012 at 2:17 AM, Arthur Zheng haoz...@gmail.com wrote: On Sun, Feb 12, 2012 at 4:34 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng haoz...@gmail.com wrote: Hi, I have downloaded and installed a local instance of galaxy on the linux server using my user account according to here: http://main.g2.bx.psu.edu/ Then I ran the following command: sh run.sh and accessed galaxy through the local firefox browser on the server http://localhost:8080 Now I am trying to use some NGS files for FASTQ Groomer. Each file is in the server disk already, but very large (~8G each). I was not able to use the upload file from your computer function under the Get Data tab (maybe because each file is too large). What am I supposed to do? Thank you! Arthur The method you tried uploads the file from your computer back to itself - making a copy as it goes with lots of overhead. You should probably consider the procedure here which allows you to avoid even making a copy on disk but point at the existing files already on the server: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Peter Hi Peter, I have followed the link you provided and selected the option Upload directory of files. Now my NGS data are in the library, and I am wondering how I can feed them to FASTQ Groomer? Thanks! Arthur You must add library files to your current history via the Shared Data menu at the top of the Galaxy window. 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/
Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer
On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng haoz...@gmail.com wrote: Hi, I have downloaded and installed a local instance of galaxy on the linux server using my user account according to here: http://main.g2.bx.psu.edu/ Then I ran the following command: sh run.sh and accessed galaxy through the local firefox browser on the server http://localhost:8080 Now I am trying to use some NGS files for FASTQ Groomer. Each file is in the server disk already, but very large (~8G each). I was not able to use the upload file from your computer function under the Get Data tab (maybe because each file is too large). What am I supposed to do? Thank you! Arthur The method you tried uploads the file from your computer back to itself - making a copy as it goes with lots of overhead. You should probably consider the procedure here which allows you to avoid even making a copy on disk but point at the existing files already on the server: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files 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/
Re: [galaxy-user] How to do BLAST on Galaxy sever?
On Thu, Feb 9, 2012 at 9:57 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Peter, It looks to me like there are versions both, with the Tool Shed version having the more recent date stamp. But if those extra functions are not needed, then yes, you are correct, the version included in the distribution would be enough. Please send corrections if I have any of this wrong, so that David gets the best information, Thanks Peter! Jen Hi Jen, I'm not sure which date stamps you are looking at, since I think it is the other way round. The NCBI BLAST+ wrappers shipped with Galaxy are currently at version 0.0.11, both in galaxy-central and galaxy-dist, dated 12 July 2011, e.g. here is the current XML file for the BLASTN wrapper: https://bitbucket.org/galaxy/galaxy-central/src/default/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml https://bitbucket.org/galaxy/galaxy-dist/src/default/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Over on the Tool Shed, Edward Kirton has a forked copy of a much older version of these wrappers at v0.0.1. The push date of 7 Jun 2011 is probably from the toolshed migration, I believe the true date is well before that. Edward added support for using local BLAST databases as a new Galaxy datatype, along with wrappers for makeblastdb and dustmasker. Assuming these have proved useful, it would make sense to merge these changes into the main BLAST+ wrappers. I have CC'd the galaxy-dev mailing list (and Edward) which is probably a better place to discuss this than the galaxy-user list. 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/
Re: [galaxy-user] How to do BLAST on Galaxy sever?
On Thursday, February 9, 2012, Jennifer Jackson j...@bx.psu.edu wrote: Hi David, It sounds like you are using the public Galaxy server at http://usegalaxy.org (http://main.g2.bx.psu.edu)? A BLAST service is not available on the public instance. (Megablast is available, but for NGS query data versus a specific set of target native genomes). Bjoern is correct that you will need to obtain a Galaxy BLAST wrapper from the Tool Shed. http://wiki.g2.bx.psu.edu/Tool%20Shed Tools Shed entries can be searched for with: http://galaxy.psu.edu/search/getgalaxy These would be installed into a local or cloud version of Galaxy and set up using the following instructions: http://getgalaxy.org Hi Jen, The NCBI BLAST wrappers used to be included as standard tools when doing a local Galaxy server installation - and were not in the ToolShed. Has that changed? 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/
Re: [galaxy-user] How can I tell what programs are used by a tool?
On Tue, Feb 7, 2012 at 9:52 PM, Beale, Holly (NIH/NHGRI) [F] holly.be...@nih.gov wrote: Hi all -- I'd like to know what programs are used when I run a tool on my data. Ideally I'd also like to know what parameters are passed to command line tools. The short answer is you can't, other than by reading the tool's documentation (ideally within Galaxy below the options), and/or reading the tool's source code (the XML file plus any scripts). Some Galaxy tools are simple wrappers for a single command line tool, in which case it is usually clear how the parameters offered to you in the Galaxy interface translate to matching command line arguments. Such Galaxy tools should make this clear in their documentation, along with giving you clear citation information for the underlying tools. Other Galaxy tools are complex scripts/tools that may call several other command line tools internally So it depends. 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/
Re: [galaxy-user] EMBOSS fuzzpro tool pattern is not read correctly from the input
On Mon, Dec 12, 2011 at 4:34 PM, domantas.motieju...@cropdesign.com wrote: Hello, I'm trying to run EMBOSS fuzzpro tool, however, I get Illegal character error '_', aparently from the fuzzpro tool itself. One of the input parameters is amino acid sequence pattern, for instance I submit AV[RL]E, but somehow it get's converted and passed to the fuzzpro as AV__ob__RL__cb__E, and then apparently these '_' are causing the error. I tested the tool on command line and it works fine. Also it works on Galaxy if I submit AVRE (just amino acid letters no special characters for pattern) So basically seems that in my input pattern string AV[RL]E the character [ is somehow converted into __ob__ and character ] is converted into __cb__ Any ideas how to fix this? Thanks, Domantas That would by Galaxy sanitising the funny characters, [ and ], and replacing them with __op__ and __cb__ which must be short for open bracket and close bracket. I believe that the fuzzpro tool (and perhaps others) need to have an explicit sanitizer and valid entry in their Galaxy wrapper XML file to allow these characters though. http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax 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/
Re: [galaxy-user] https://galaxy.jgi-psf.org/
On Mon, Nov 14, 2011 at 10:08 PM, Chauhan, Archana achau...@utk.edu wrote: Dear Sir/Madam, I am registered with galaxy http://main.g2.bx.psu.edu/. But I recently came across another link as https://galaxy.jgi-psf.org/ . This has some very good applications especially w.r.t to the genome assembly (MIRA, velvet), microbial ecology (Mothur etc) and Stats/Graphing Tools. Overall this links seems much better than the Main galaxy and fulfils the general aspirations of a user. Is this link subscribed JGI and its collaborators OR any one can be a part of it. Is there any version of galaxy server wherein we can have these applications available for public use. Thank you. Tools like MIRA and Velvet can be extremely demanding to run, so are dangerous/expensive to offer on a public Galaxy. I don't know who exactly runs https://galaxy.jgi-psf.org/ and if they intend it to be available for external usage. I wrote the MIRA wrapper for our in house use with viral genomes (small enough not to be a big computational load) and published it on the Galaxy toolshed for others to use too in their own Galaxy servers. It is nice to see it being used on https://galaxy.jgi-psf.org/ and it looks like they have a pretty powerful cluster with big memory machines with 500GB of RAM, which should cope with many MIRA work loads. If you have a local Galaxy at your department/institute then try asking them if they can install this and other tools of interest for you. Regards, 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/
Re: [galaxy-user] Question about file formats
On Thu, Nov 10, 2011 at 6:10 PM, Rena Zheng rzh...@mail.med.upenn.edu wrote: Hi, I uploaded a bed file to Galaxy and did some text manipulations. I want to download the new file as a bed format that I can then open up in excel or a text editor. However, when I save the data, it is a .tabular format that I cannot open with these programs. What should I do? Thanks, Rena Try renaming the file to end with .tsv or .txt and Excel or your text editor should be happy. 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/
Re: [galaxy-user] selecting reads at random from fastq file
On Tue, Nov 8, 2011 at 9:57 PM, Austin Paul austi...@usc.edu wrote: Hi, I am curious if anyone knows how to select random lines from a fastq file. There is a select random lines tool in text manipulation tools, but it does not treat fastq files specifically, so it will not group quality lines with sequence lines. And if I turn the fastq file to tabular form in order to select lines, I can no longer return it to fastq form. Anyone know a way to do this in galaxy? Otherwise, perhaps another program? Thanks. Austin How big are your FASTQ files (can they be indexed in memory)? And are you willing to program? If you like Python, Biopython's Bio.SeqIO.index(...) or Bio.SeqIO.index_db(...) functions would let you do this easily. Have a look at the Getting the raw data for a record example in the tutorial, and please ask if you liked a little more help: http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.pdf Regards, 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/
Re: [galaxy-user] selecting reads at random from fastq file
On Tue, Nov 8, 2011 at 10:26 PM, Austin Paul austi...@usc.edu wrote: Hi Peter, Thanks for the suggestion. For example, I have a fastq file with 50 million reads and I want to randomly select 5 million of them. It seems biopython would very easily select a single or a handful of reads with the Bio.SeqIO.index() function. Would it also be able to do the job I am interested in? Austin I think so, but you'd have to use Bio.SeqIO.index_db() which stores the index in an SQLite dictionary rather than in memory which isn't really viable here (unless you have a 64bit big memory machine?). I don't think I've tried it with quite that many reads though... Alternatively, if I understood her correctly, Jennifer pointed out you can do this in Galaxy but it will take a lot of IO: 1. Convert FASTQ to tabular (4 lines per record - 1 line per record) 2. Randomly select lines (each line is now a record so safe) 3. Convert tabular back to FASTQ It should work though, and requires no additional programming. 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/
Re: [galaxy-user] fastq groomer
On Tue, Nov 1, 2011 at 4:58 PM, Kevin Lam abou...@gmail.com wrote: actually Illumina 1.8+ has one more quality value higher than fastqsanger (see http://en.wikipedia.org/wiki/FASTQ_format ) my question now I guess is if I use fastqsanger would it break anything when it encounters the 'J' in the qual values? The Sanger FASTQ format has always allowed J (PHRED 41), the issue is some tools might treat that as an error as it is unusually high for a raw read. For instance, you need at least FASTX v0.0.13 to cope with this - older versions didn't like it. http://seqanswers.com/forums/showthread.php?p=49667 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/
Re: [galaxy-user] Problem with bam and/or bai files
Sending to galaxy-dev ... On Thu, Oct 27, 2011 at 5:51 AM, Jim Robinson jrobi...@broadinstitute.org wrote: Hi Mike, Someone from the Galaxy team can perhaps give some insight on what went wrong, I can comment on the error message from IGV. That error is thrown from Picard, in every case I've investigated so far it was traced to a problem with the index. Useful background re: Error reading bam file. This usually indicates a problem with the index (bai) file. ArrayIndexOutofBoundsException: 4682 (4682). The most common causes are (1) a problem with the sequence dictionary in the BAM header itself, specifically incorrect sequence lengths, Any idea what tools produce that kind of thing? and (2) indexing an un-sorted BAM. Apparently samtools will make invalid indexes from such files without any complaints in both cases. You can even use samtools tview on such files, it happily will show you some random region when you query. That is news to me - I recall samtools index being recommended as a way to determine if a BAM files was sorted or not (error on unsorted, you get an index if it was sorted) and again from memory this is what Galaxy uses internally as part of preparing BAM files on upload. Might this be tied to a specific version of samtools? e.g. a possible regression? I don't see a Sort step in your workflow, maybe that's the problem? Please CC me on any reply, I might miss it in the list. Jim Thanks, 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/
Re: [galaxy-user] tool.xml console redirection within command-tag
On Mon, Oct 24, 2011 at 9:01 AM, Appelt, Uwe uwe.app...@nct-heidelberg.de wrote: Dear all, that has probably been asked 10e6 times, however, I don't find any comments on how to properly escape special characters in a toolxy.xml. What I want to achieve is the following: command interpreter=bash$myScript $logFile/command where myScript is dynamically created (as part of the configfiles-section) and the logFile is where stderr and stdout should go to. Now the problem is obviously the -character, because it causes the following error-msg on reloading the toolxy.xml: ExpatError: not well-formed (invalid token): line 5, column 50 where the 5/50 refers to the -character. By the way: redirecting either stdout or stderr by specifying just (instead of ) works fine. I tried a lot of different notations in the meanwhile, but neither something like \ nor \amp; works. Any suggestions? Many thanks in advance and Cheers! Uwe Don't you need to escape both the and the characters here? i.e. amp;gt; should work. 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/
Re: [galaxy-user] tool.xml console redirection within command-tag
On Mon, Oct 24, 2011 at 9:42 AM, Appelt, Uwe uwe.app...@nct-heidelberg.de wrote: Hi Peter, thanks a lot for your quick reply. However amp;gt; doesn't seem to work as well. Also, I do have to admit that two different doesn't work exist. Notations that are not accepted during parsing of toolxy.xml: \ \\ Notations that are accepted, but don't produce any content written to $logFile: amp; amp;gt; #38;#62; Any other suggestions? Cheers, Uwe Curious. Well, at least you seem to have valid XML now (double check this with an XML validator). Does Galaxy capture anything in the info box (stdout)? There are some variants like 21 for redirecting stderr to stdout, try combining that with logfile. My *guess* however is the interpreter=bash may be to blame, try this after ensuring the script is executable and on the path or fully specified: command$myScript amp;gt; $logFile/command Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] tool.xml console redirection within command-tag
Hi Uwe, On Mon, Oct 24, 2011 at 10:47 AM, Appelt, Uwe uwe.app...@nct-heidelberg.de wrote: Hi again, yes, you're right. The problem source is something else. As soon as I specify one of the following command interpreter=bash$hisapWrapperScript amp;gt; $logFile/command command interpreter=sh$hisapWrapperScript amp;gt; $logFile/command commandbash $hisapWrapperScript amp;gt; $logFile/command commandsh $hisapWrapperScript amp;gt; $logFile/command I get a according debug-line in the galaxy.log, reporting something like: galaxy.jobs.runners.local DEBUG 2011-10-24 11:26:55,360 executing: bash /home/extuser/www/galaxy/galaxy_working/database/job_working_directory//tmpZmFMfg /home/extuser/www/galaxy/galaxy_working/database/files/005/dataset_5410.dat So the definitely makes it through XML, Cheetah, etc. -parsers and finally to the cmd-line. However, neither BASH nor SH produce a log-file as intended. You didn't try the precise combination I meant, command$hisapWrapperScript amp;gt; $logFile/command where $hisapWrapperScript is marked as executable and has a Unix hashbang line saying which shell to use, e.g. #!/usr/bin/bash Apologies if I was too vague. For some strange reason (Peter, you're right again) all log-lines appear in the green box. To be expected, Galaxy captures any stdout (assuming nothing else captured it first) and puts it in the info field. And even more, the green box turns of course red as soon as something is written to stderr. Yes, it is a long standing Galaxy bug that any stderr out is treated as an error condition, rather than looking at the return code: https://bitbucket.org/galaxy/galaxy-central/issue/325/ Aah, but the different redirection syntax works. So to conclude: command interpreter=bash$hisapWrapperScript gt; $logFile 2gt;amp;1/command works like a charme - problem solved! Thanks Peter!!! Cheers, Uwe Glad you got there in the end :) Peter By the way - this whole discussion would have been better suited to the galaxy-dev list (CC'd) since it is about developing tools for Galaxy rather than Galaxy end users. ___ 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] Patch for better FASTQ description handling
On Thu, Oct 20, 2011 at 2:15 PM, Eric Cabot ca...@biotech.wisc.edu wrote: I was not aware of this new naming. It seems like a terrible decision from Illumina because now both reads in a pair technically have the same ID (but a different description). This is not quite the case. Here are two fastq header lines for a pair of reads produced by Illumina's CASAVA 1.8: @XYZZY:123:D0ABCDEFG:7:1101:1445:2057 1:N:0:CTTGTA @XYZZY:123:D0ABCDEFG:7:1101:1445:2057 2:N:0:CTTGTA Yes, Illumina gives both read 1 and read 2 the same template ID of XYZZY:123:D0ABCDEFG:7:1101:1445:2057 (much like the two reads would have the same ID in a SAM/BAM file). The two key things to note, relevant to this discussion are: 1. A space character is used to split the fields into two groups. This is actually a good thing, because that particular character can NEVER appear in either a sequence or a quality line. This make it easy to detect name lines as those beginning with @ (a valid quality character) and also having a space. If you are writing a parser for the new Illumina fastq format, please don't break the names on spaces! Yes, you could use the space as a sanity test for *this* style Illumina FASTQ, and have a bespoke parser which treats this all specially. But for a generic FASTQ parser you *should* split at the space. The point is Illumina have changed the meaning of their FASTQ identifier, it used to be the template ID plus a /1 or /2 suffix, but now it is just the common template ID used for both parts. 2. Appart from the read number, encoded as the digit immediately following the space, the two lines are identical--as they were with earlier CASAVA versions. Why is this worse than two lines differing by /1 vs. /2? Because it is a change from the existing well established convention, which will require changed to hundreds of scripts and and tools (guessed number including user's bespoke scripts). An additional improvement with the new naming convention is that flowcell and run ID's, as well as a flag for not passing filters (where N means does PF), are now included. Yes, that is good. 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/
Re: [galaxy-user] Patch for better FASTQ description handling
On Wed, Oct 19, 2011 at 4:53 AM, Florent Angly florent.an...@gmail.com wrote: I have had the chance to try the patch on several datasets and it looks good :) I reiterate my suggestion to pull the patch in galaxy-central. Best, Florent It looks sensible, although I would add a comment to the join method to say the description from read1 is taken (if the reads differ in their descriptions). Mind you, the whole module seems to lack docstrings ;) Are there any unit tests (not that Galaxy seems to insist on them)? 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/
Re: [galaxy-user] Galaxy and Ion Torrent
2011/9/28 cuentasecuenciacion secuenciac...@ipb.csic.es: Hello!! Does anybody know whether Ion Torrent data is supported by Galaxy? Thank you!! IonTorrent data acts a lot like Roche 454, it even comes as SFF files (or FASTQ). So in principle anything Galaxy supports for 454 would be worth trying with IonTorrent data. 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/
Re: [galaxy-user] Getting (or setting) physical file name
On Thu, Sep 15, 2011 at 6:11 PM, Paul-Michael Agapow paul-michael.aga...@hpa.org.uk wrote: So one of my colleagues has a script he wants to turn into a Galaxy tool. The twist is that script: 1. Looks for files with a fixed name (e.g. “params.txt”) 2. Accepts other file names as commandline arguments, but the actual names of those files has arguments embedded in it (e.g. “nuc_100iter_b.fasta” for nucleotide data in fasta format to be run against model b for 100 iterations.) I know, awkward and clumsy. But hardly unique for many historical bioinformatic tools. Anyway, the challenge for me is to pick the easiest path to port this script to a tool. And it seems to be fairly awkward under the Galaxy model as I understand it. Possibilities: 1. Rewrite the script argument parsing and invocation. Obviously, there will be resistance to this and with some justification (“I thought you said this could wrap any command line program …”) If this is your own tool, this is the cleanest solution and helps beyond just using it within Galaxy. 2. Write a script that calls the original script after moving and renaming files according to desired arguments. Any problems with a two-script/executable tool like this? That's what I'd go for - a wrapper script which takes command line arguments like a sane command line tool, and uses them to prepare the input files for the weird script. Your tool should automatically be called from a temp working directory so you can probably just make the specially named files right there, and try using links to alias the input files rather than copying them (faster as less IO). How do I specify the interpreter for both parts of the script? If your script is marked as executable with a suitable hash bang, it doesn't even need the Galaxy interpreter in the XML file. For the internal script it doesn't matter at all - Galaxy doesn't need to know. 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/
Re: [galaxy-user] Installing Galaxy on my computer
On Mon, Sep 12, 2011 at 5:20 PM, Lilach F lilac...@gmail.com wrote: Hi Jennifer, I already tried 2 weeks ago to upload my whole exome data by FTP, according to the instructions you sent below. The files are too big, it should take days for each file, and it always stops in the middle after 12 hours or so. So I gave up. If I use Galaxy on a cloud, I can work with the files on my computer, or I will still have to upload them by ftp? I guess I will still have to upload them, so it doesn't solve my problem? If you use Amazon, they have a service where you can post them a hard drive and they copy it onto their cloud for you. This costs money of course, but avoids the network problem. The other option is to check with your local computing people - perhaps there is a cluster or local super computing group you can get access to? 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/
Re: [galaxy-user] running cufflinks
On Tue, Sep 6, 2011 at 9:29 PM, Peng, Tao tp...@fhcrc.org wrote: Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY ensemble were recognized by GALAXY cufflinks as a GTF file although they all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as GFF files? Thx, I'm pretty sure Galaxy ignores the original filename extension (it will be stored on disk as *.dat once uploaded to Galaxy). If you could post the start of each file (or links to the complete files) that would be very helpful for working out why Galaxy has misidentified the GTF files as GFF. 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/
Re: [galaxy-user] mi-tools- tools_fabfile.py permissions requirements (local install)
Note: Local install questions are normally directed to the galaxy-dev list (CC'd) rather than galaxy-user On Mon, Aug 1, 2011 at 3:21 PM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Enis, a few things we came across: a, local install R - not the correct download url, Which URL are you talking about? The wiki page on dependencies http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies correctly links to the R project as http://www.r-project.org/ rpy - will this be fixed? What needs to be fixed? Moving Galaxy to rpy2? https://bitbucket.org/galaxy/galaxy-central/issue/103/upgrade-rpy-to-latest-version permissions: the script seems to use sudo and galaxy interchangeably, which creates an issue with permissions writing to folders. Is there a way to install as galaxy user only? Do you mean installing Galaxy without admin rights (i.e. without using sudo)? If we do need the switching between sudo and galaxy - is there a set of directory permissions you suggest for the original galaxy-dist install and the galaxyToools folder? Good question - having manually reset permissions on a test server while debugging driving mappings, I'd like to know what they should be. Are you planing on using the Linux user group functionality as part of your setup? e.g. Both your personal account and the Galaxy user account could be part of a Galaxy admin group. b, as a second category of questions: are there any tools that do not work on the standard cloud install? (skipped over entirely or installed but do not work?) By that do you mean of the standard tool set in the main repository? (Because there will be lots of Galaxy tools in the Tool Shed which are not in the standard cloud install). 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/
Re: [galaxy-user] BAM files loading and mandatory grooming
2011/7/27 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hello Jennifer, Aaaah so the grooming means creating the .bai file? Ok, I didn't know, thanks for the information. But that leaves me wondering why it is necessary to copy the data (unless the alignments are not sorted yet, which is possible knowing where the data comes from). I won't have much time left to look into it but if I can I'll let you know. Thanks, L-A Sadly samtools sort doesn't set the header information, so it is not enough to look at that to say if and how a SAM/BAM file is sorted. I think what the Galaxy code does now is attempt to index the BAM file (as a safe way to find out if is really is suitably sorted), and if that fails sorts it by co-ordinate (which will make a new BAM file) and then indexes the sorted version. 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/
Re: [galaxy-user] blastn: NameError: name 'cmd' is not defined
On Fri, Jul 1, 2011 at 4:35 PM, Sergei Ryazansky s.ryazan...@gmail.com wrote: Thanks for answer, but I have just updated the galaxy source code and blastn works fine! Sorry for any inconvenience :) It was an error in the wrapper script's error handler, already fixed. 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/
Re: [galaxy-user] FTP and command line access in Galaxy
On Wed, Jun 22, 2011 at 6:47 AM, Robert Curtis Hendrickson curt...@uab.edu wrote: Nate, The Galaxy’s ability to pull files with user/password from FTP sites as a client is great. However, I need to pull data from an HTTP site at a sequencing center with user/password (already tried to get them to set up an FTP server, no luck). Any way to do this? Try asking the sequencing centre if the username and password can be provided as part of the HTTP URL, then give that URL to Galaxy. 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/
Re: [galaxy-user] suggestion for multithreading
2011/6/2 Nate Coraor n...@bx.psu.edu: Hi Louise-Amélie, I haven't done anything with this code yet, but I wanted to let you know that we'll eventually be adding it, I'm just going to change the implementation slightly. I'd like to merge the functionality of the csv into an xml config I'm already working on (but haven't yet fully decided on the syntax). And it should be possible for tools to access these parameters in the command line template. A lot of our NGS tools have the number of threads to use hardcoded in the tool config, which is bad. --nate On a related point, I've previously suggested a $variable could be defined for use in tool XML wrappers to set the number of threads. This number could come from a general configuration file, or perhaps via the cluster settings - the point is the tool doesn't need to know, it just gets told how many threads it is allowed. 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/
Re: [galaxy-user] (no subject)
On Tue, May 24, 2011 at 12:40 AM, Aaron Jex a...@unimelb.edu.au wrote: Hi, Can’t seem to find an answer to this on your wiki site and it’s not in the tutorial. I would like to filter my 454 reads for high quality regions, rename the resulting sequence fragments AND relink the new reads (fragments) to the original quality data so that I can take these filtered reads and assembly them using MIRA. Is there a way to do this with Galaxy? See Alex's answer. So basically all I want to do is take the new read fragments I get from converting the tabular file to the fasta file as shown in your metagenomics tutorial, and generate a corresponding qual file for these ‘new’ reads. When working in Galaxy, I use the SFF converter tool to make FASTQ rather than FASTA and QUAL. MIRA will also read in FASTQ, and I find that is easier to work with for filtering and trimming than a matched FASTA and QUAL file. 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/
Re: [galaxy-user] Text Manipulation: Filter out duplicates (uniq) from an plain text file ?
On Fri, May 6, 2011 at 3:16 PM, Roman Valls brainst...@nopcode.org wrote: Well, having similarly basic tools (in Galaxy) that can be performed on the commandline, such as sort or cut I just wondered how come a uniq is not there on the tool panel in some form/name. Thanks for the feedback Rory ! That's a timely question - I was also looking for something within Galaxy to take a text file and remove duplicate lines. 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/
Re: [galaxy-user] quality stat.
On Tue, May 3, 2011 at 10:00 AM, Robin Mjelle robinmje...@gmail.com wrote: Dear User, I am trying to use the tool Compute quality statistics in galaxy on Ilumina single reads. The file is 2.3 Gb, fastq format. I have performed Quality format converter on the data set and the format is now qualillumina. Despite of this, galaxy don't recognize any dataset in the workflow to use as input into quality statistics. Any idea why my dataset is not accepted as input? Best, Robin Looking at the XML wrapper, it expects fastqsanger ONLY. See fastx_toolkit/fastx_quality_statistics.xml It could in theory take fastqillumina or fastqsolexa as well, I thought there was an open bug report on this issue but I can't find it right now. Certainly fastx_clipper.xml was updated to use the -Q 33 switch only for Sanger quality scores, and from a quick check all the other FASTX tools have this fix except fastx_quality_statistics.xml 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/
Re: [galaxy-user] BAM files
On Wed, Apr 20, 2011 at 4:00 AM, Edward Dudley egd...@psu.edu wrote: Hi - I have a set of 454 reads that have been trimmed and converted to BAM format using Galaxy, and I can visualize the alignment with E. coli genomes using the UCSC browser. Problem is, I'd like to display the alignment in Artemis, but Artemis doesn't seem to want to read the .BAM file downloaded from Galaxy; I can import my genome sequence but when trying to import the BAM a blank window with message in the header keeps popping up. Anyone else tried to do this, and is there something about the Galaxy BAM files that Artemis doesn't like? Thanks. Ed Artemis will need the BAM index file (the BAI file). It may also insist on the normal extensions, *.bam and *.bai or *.bam.bai (but not *.dat) 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/
[galaxy-user] Combining tables with different numbers of columns
Hi all, I'm having a little trouble understanding the best way to perform some tabular file manipulations in Galaxy. I have several tabular files, which contain different numbers of columns, which I want to combine using a single column containing an identifier (which must match for the rows to be combined). e.g. File 1 contains, c1 = ID c2 = Score1a File 2 contains, c1 = ID c2 = Score2a c3 = Score2b c4 = Score2c File 3 contains, c1 = ID c2 = Score3a c3 = Score3b Desired combined file containing: c1 = ID c2 = Score1a c3 = Score2a c4 = Score2b c4 = Score2c c6 = Score3a c7 = Score3b I have worked out how to do this with two calls to the Join two Datasets tool, but this results in the repetition of the join column (ID in this example), so a final clean-up is required using the Cut tool (which breaks the column assignments). The more flexible Column Join tool would let me combine an arbitrary number of files, but is designed for input files containing the same column structure. Is there a better way to do this with Galaxy as it stands? Alternatively, would adding an option to the Join two Datasets tool not to bother with the redundant column be widely useful? 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/
Re: [galaxy-user] FASTQ to FASTQSanger using Groomer question
On Mon, Mar 21, 2011 at 1:42 PM, David K Crossman dkcro...@uab.edu wrote: Hello! I am fairly new to using Galaxy and have a question about the FASTQ Groomer feature. I have 4 RNA-Seq raw data files that were just recently generated from Illumina’s NGS instruments. Very recently? If they are already using Illumina's CASAVA v1.8 pipeline then the FASTQ files will already be in the Sanger FASTQ format: http://seqanswers.com/forums/showthread.php?t=8895 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/
Re: [galaxy-user] local directory
On Fri, Mar 11, 2011 at 10:07 PM, Albert Ayoub albert.ay...@yale.edu wrote: I installed Galaxy on my own linux machine. I would like to perform analysis on local RNAseq files since they are too big to upload. How do we add files from a local directory or a network share? Providing you are a Galaxy admin, and the import from file system feature is enabled in universe.ini then you can do this as a shared data library. See e.g. https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibrarySecurity 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/
Re: [galaxy-user] Quality Score
Great :) Don't forget to CC the mailing list in future ;) On Fri, Feb 25, 2011 at 4:46 PM, Amy Boddy abo...@med.wayne.edu wrote: Thank you, these articles helped! On Thu, Feb 24, 2011 at 5:47 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Feb 24, 2011 at 8:47 PM, Amy Boddy abo...@med.wayne.edu wrote: Hello, I was wondering how Galaxy calculates the quality score for NGS data? Is there any documentation I could read on how this is calculated? Thanks! -Amy Boddy Which quality score are you talking about? Raw reads? Mappings? If it's FASTQ files you mean, may I suggest: http://dx.doi.org/10.1093/nar/gkp1137 and http://en.wikipedia.org/wiki/FASTQ_format Peter -- Amy Boddy Ph.D Candidate Center for Molecular Medicine Genetics Wayne State University School of Medicine 540 E. Canfield, Detroit MI 48201 Website: http://homopan.wayne.edu/ Phone: 313.577.0086 email: abo...@med.wayne.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 other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Is there any tool in Galaxy for trimming the Barcode in 454 sequencing data? Thanks.
On Mon, Feb 28, 2011 at 9:28 PM, Yang Liu ywl5...@psu.edu wrote: Is there any tool in Galaxy for trimming the Barcode in 454 sequencing data? Thanks. Hi, The Roche off instrument applications cover this (working directly with the SFF files). Try asking Edward Kkirton if he would update his Suite of Newbler tools wrappers in the Community Tool Shed to handle barcode trimming (and dividing SFF files by barcode). See http://community.g2.bx.psu.edu/ Alternatively, and maybe not quite what you need, I'm working on barcode/primer/adapter trimming for FASTA, FASTQ and SFF files - see this thread earlier this month on the Galaxy dev mailing list: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-February/004344.html 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] Quality Score
On Thu, Feb 24, 2011 at 8:47 PM, Amy Boddy abo...@med.wayne.edu wrote: Hello, I was wondering how Galaxy calculates the quality score for NGS data? Is there any documentation I could read on how this is calculated? Thanks! -Amy Boddy Which quality score are you talking about? Raw reads? Mappings? If it's FASTQ files you mean, may I suggest: http://dx.doi.org/10.1093/nar/gkp1137 and http://en.wikipedia.org/wiki/FASTQ_format 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] 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] FASTQ type change
On Thu, Feb 10, 2011 at 6:42 PM, Peter wrote: On Thu, Feb 10, 2011 at 6:34 PM, Stephen Taylor wrote: Sounds like this should be added into the main release. It would save a lot of time/disk space instead of using Groomer. I agree. Maybe Dan can take care of it - I don't have bowtie setup on our local Galaxy (yet) so I wouldn't be able to test the proposed fix. In the long term however the Solexa/Illumina FASTQ formats are on their way out since CASAVA 1.8 will switch to the Sanger FASTQ encoding: http://seqanswers.com/forums/showthread.php?t=8895 Hi Stephen, Maybe you should file an issue on bitbucket about extending the Bowtie wrapper to support fastqillumina as well as fastqsanger as input? https://bitbucket.org/galaxy/galaxy-central/issues?status=newstatus=open The current version of the wrapper is here if you want to look at it: https://bitbucket.org/galaxy/galaxy-central/src/default/tools/sr_mapping/bowtie_wrapper.xml 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/
