[galaxy-dev] Fwd: MACS failed because of lambdaset options
...moved to dalaxy-dev, since it is about your local Galaxy instances: Hi Philippe Your galaxy wrapper for MACS expects version 1.3, where the option --lambdaset is present. (see https://github.com/taoliu/MACS/blob/macs_v1/ChangeLog) Regards, Hans-Rudolf Original Message Subject:[galaxy-user] MACS failed because of lambdaset options Date: Mon, 29 Oct 2012 11:40:28 +1100 From: Philipe Moncuquet philippe.m...@gmail.com To: galaxy-u...@lists.bx.psu.edu Hi, I am trying to use MACS and I get the following error when the job fails : Usage: macs -t tfile [-n name] [-g genomesize] [options] Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks macs: error: no such option: --lambdaset I am not really familiar to MACS so I checked the documentation and it seems Galaxy is rigth to complain because there is no such option as --lambdaset (http://liulab.dfci.harvard.edu/MACS/README.html). I went back to the xml wrapper and there is this ( paramname=lambdasettype=text ) parameters that corresponds to the text box 3 levels of regions around the peak region to calculate the maximum lambda as local lambda: Does anyone face the same problem ? Any clue on what I should try, should I modify the wrapper ? Cheers, Philippe ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How are jobs managed on single machine?
Hi Jim If using a standalone server, Galaxy is using its own queuing system, which you can modify by changing (in universe_wsgi.ini): local_job_queue_workers user_job_limit but the system is not aware of the memory size and number of cores. In your specific example, running out of memory is probably the bigger issue. Hope this helps, Hans-Rudolf On 10/26/2012 01:41 PM, James Vincent wrote: Hello, I cannot seem to find the details on how jobs are managed when Galaxy is run on a standalone server. Are jobs managed in a queue of some sort? Does Galaxy determine resources available in some way and moderate jobs that are run? As a specific example, we have a 40 core machine with 1TB of memory. If 10 users each submit 10 jobs each, say for a bowtie job that has been set to use 8 cores, will Galaxy sort this all out and only run jobs to fill the 40 cores? Are there settings to control this behavior without installing an external job manager like SGE? Thanks, Jim ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How are jobs managed on single machine?
On 10/29/2012 11:33 AM, James Vincent wrote: Thanks very much. Sorry for the double post - my first was rejected due to wroneg email, but I guess it made it through. Do you happen to know if one can query the number of jobs queued and running? I'd like to put status monitor somewhere for regular users. I think this will cut down on the number of emails back to me asking why jobs are not running. :) use the 'report tool', see: reports_wsgi.ini and run_reports.sh Hans-Rudolf Jim On Mon, Oct 29, 2012 at 4:09 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Jim If using a standalone server, Galaxy is using its own queuing system, which you can modify by changing (in universe_wsgi.ini): local_job_queue_workers user_job_limit but the system is not aware of the memory size and number of cores. In your specific example, running out of memory is probably the bigger issue. Hope this helps, Hans-Rudolf On 10/26/2012 01:41 PM, James Vincent wrote: Hello, I cannot seem to find the details on how jobs are managed when Galaxy is run on a standalone server. Are jobs managed in a queue of some sort? Does Galaxy determine resources available in some way and moderate jobs that are run? As a specific example, we have a 40 core machine with 1TB of memory. If 10 users each submit 10 jobs each, say for a bowtie job that has been set to use 8 cores, will Galaxy sort this all out and only run jobs to fill the 40 cores? Are there settings to control this behavior without installing an external job manager like SGE? Thanks, Jim ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Trackster and gff file with multiple chromosome annotations
Whatever the file type I set for the gff file (gff3, gff or gtf), I get the transcript_id error: Traceback (most recent call last): File /home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py, line 91, in main() File /home/pgtgal/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_fli.py, line 30, in main for feature in read_unordered_gtf( open( in_fname, 'r' ) ): File /home/pgtgal/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py, line 375, in read_unordered_gtf transcript_id = line_attrs[ 'transcript_id' ] KeyError: 'transcript_id' This was due to an incomplete feature. Turns out that GFF support hadn't been included in feature search; I've added it in -central changeset fa045aad74e9: https://bitbucket.org/galaxy/galaxy-central/changeset/fa045aad74e90f16995e0cbb670a59e6b9becbed Is the gff file not correct? I believe there is an issue with your GFF: it is using non-standard identifiers in the attributes (last) column. To the best of my knowledge, 'name' is not a valid field for connecting features in GFF3 (which is my best guess for the file version), but your GFF uses this field anyways. To fix this issue, I replaced 'name' with 'ID' (which is compliant GFF3) from the command line: -- % sed s/name/ID/ ~/Downloads/test.gff ~/Downloads/test_with_ids.gff -- and this fixed the issue. Finally, there is a sed wrapper in the toolshed should you want to do this conversion in Galaxy: http://toolshed.g2.bx.psu.edu/repository/browse_categories?sort=nameoperation=view_or_manage_repositoryf-deleted=Falsef-free-text-search=sedid=9652a50c5a932f3e Best, J.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] MrBayes wrapper - set parameters through Galaxy?
Hello all, I've written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with $ mb and then enter your commands, or directly execute a Nexus file (containing the data and commands) with $ mb nexusfilename. Please correct me if I'm missing something or thinking about this completely wrong. I'd appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.go...@agr.gc.ca mailto:ann.go...@agr.gc.ca Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?
Ann, I think you may be able to do this by generating another nexus file using configfiles in the Galaxy tool config which just contains a command block, similar to the example here: http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F -- jt On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann ann.go...@agr.gc.ca wrote: Hello all, I’ve written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with “$ mb” and then enter your commands, or directly execute a Nexus file (containing the data and commands) with “ $ mb nexusfilename”. Please correct me if I’m missing something or thinking about this completely wrong. I’d appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.go...@agr.gc.ca Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Error while uploading data from local directory
This is a bug that is fixed in revision ecd131b. Sorry for the inconvenience. -- jt On Sat, Oct 27, 2012 at 6:12 PM, Luciano Cosme cosme.sim...@gmail.com wrote: Howdy, I installed galaxy in a new server that I build and I am getting the following error when I try to upload the files from a local directory. Error attempting to display contents of library (A.aegypti_mRNA): (OperationalError) no such column: True u'SELECT dataset_permissions.id AS dataset_permissions_id, dataset_permissions.create_time AS dataset_permissions_create_time, dataset_permissions.update_time AS dataset_permissions_update_time, dataset_permissions.action AS dataset_permissions_action, dataset_permissions.dataset_id AS dataset_permissions_dataset_id, dataset_permissions.role_id AS dataset_permissions_role_id XnFROM dataset_permissions XnWHERE True AND dataset_permissions.action = ?' ['access']. My raw data is stored in a different hard drive and I am just linking them to Galaxy. I also changed the permissions recursively in the folder where the data is (777). Any help will be appreciated. Thank you. Luciano -- Luciano Cosme - PhD Candidate Texas AM Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 co...@tamu.edu - ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?
Brilliant, thanks! I had seen the FAQ, but didn't know about configfiles. Much appreciated! Ann -Original Message- From: ja...@taylorlab.org [mailto:ja...@taylorlab.org] On Behalf Of James Taylor Sent: Monday, October 29, 2012 2:03 PM To: Gomez, Ann Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy? Ann, I think you may be able to do this by generating another nexus file using configfiles in the Galaxy tool config which just contains a command block, similar to the example here: http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F -- jt On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann ann.go...@agr.gc.ca wrote: Hello all, I've written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with $ mb and then enter your commands, or directly execute a Nexus file (containing the data and commands) with $ mb nexusfilename. Please correct me if I'm missing something or thinking about this completely wrong. I'd appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.go...@agr.gc.ca Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?
Ann, Also to your request I'd appreciate any input about MrBayes or a similar kind of tool. We are developing a suite of tools for phylogenetics in Galaxy. We are calling the tool suite Osiris. We are currently adding the full tool suite to Bit Bucket: https://bitbucket.org/repo/all?name=osiris_phylogenetics and many tools are on the tool shed under a repository called ucsb_phylogenetics. We are describing some of the tools here: http://osiris-phylogenetics.blogspot.com/ We are in rather active development right now, but the RAxML tools have been used rather extensively, and allow some interactive choices (model choice, bootstrap reps, DNA v Protein, etc). We also have a tool for BEAST (very simple, just passes the formatted xml file to run the program through Galaxy). Another phylogenetic tree estimation tool on the tool shed (not ours) exists for GARLI. We plan to develop a tool for MrBayes, as well, but perhaps we will not have to anymore! Best wishes, Todd Oakley On 10/29/2012 11:43 AM, Gomez, Ann wrote: Brilliant, thanks! I had seen the FAQ, but didn't know about configfiles. Much appreciated! Ann -Original Message- From: ja...@taylorlab.org [mailto:ja...@taylorlab.org] On Behalf Of James Taylor Sent: Monday, October 29, 2012 2:03 PM To: Gomez, Ann Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy? Ann, I think you may be able to do this by generating another nexus file using configfiles in the Galaxy tool config which just contains a command block, similar to the example here: http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F -- jt On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann ann.go...@agr.gc.ca wrote: Hello all, I've written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with $ mb and then enter your commands, or directly execute a Nexus file (containing the data and commands) with $ mb nexusfilename. Please correct me if I'm missing something or thinking about this completely wrong. I'd appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.go...@agr.gc.ca Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- *** Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA *** Lab Website http://labs.eemb.ucsb.edu/oakley/todd/ Twitter: @UCSB_OakleyLab *Recent Papers: * * Pancrustacean Phylotranscriptomics MBE Paper http://mbe.oxfordjournals.org/content/early/2012/09/12/molbev.mss216.abstract * Convergent Evolution in Cephalopoda BMC Ev Biol http://www.biomedcentral.com/1471-2148/12/129/abstract * Cnidocyte discharge regulated by opsin and light BMC Biology Paper http://tinyurl.com/7dajl2q Scientific American Write-up http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/ * Sponge Larvae Could be Guided by Cryptochrome J Exp Biol. Paper http://jeb.biologists.org/content/215/8/ii | Nature News http://www.nature.com/nature/journal/v484/n7393/full/484145d.html ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?
On Oct 29, 2012, at 3:20 PM, Todd Oakley todd.oak...@lifesci.ucsb.edu wrote: Ann, Also to your request I'd appreciate any input about MrBayes or a similar kind of tool. We are developing a suite of tools for phylogenetics in Galaxy. We are calling the tool suite Osiris. We are currently adding the full tool suite to Bit Bucket: https://bitbucket.org/repo/all?name=osiris_phylogenetics and many tools are on the tool shed under a repository called ucsb_phylogenetics. We are describing some of the tools here: http://osiris-phylogenetics.blogspot.com/ We are in rather active development right now, but the RAxML tools have been used rather extensively, and allow some interactive choices (model choice, bootstrap reps, DNA v Protein, etc). We also have a tool for BEAST (very simple, just passes the formatted xml file to run the program through Galaxy). Another phylogenetic tree estimation tool on the tool shed (not ours) exists for GARLI. We plan to develop a tool for MrBayes, as well, but perhaps we will not have to anymore! Best wishes, Todd Oakley This is an interesting project. I'm glad to see more people working on phylogenetics related wrappers and workflows. I wonder if we could get a Phylogenetics category added to the main Galaxy Toolshed, so we could put all the relevant wrappers in there to make them easier to find considering the apparent duplication of efforts. Regards, Alex___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?
On Oct 29, 2012, at 4:40 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: This is an interesting project. I'm glad to see more people working on phylogenetics related wrappers and workflows. I wonder if we could get a Phylogenetics category added to the main Galaxy Toolshed, so we could put all the relevant wrappers in there to make them easier to find considering the apparent duplication of efforts. Good idea, the main toolshed now has a Phylogenetics category. -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?
Hi Alex, Todd; thanks for the info and links! The Garli tool looks a lot more sophisticated than what I have so far, so I'm sure it will be helpful to look at. Ann -Original Message- From: Oleksandr Moskalenko [mailto:o...@hpc.ufl.edu] Sent: Monday, October 29, 2012 4:26 PM To: Gomez, Ann Cc: galaxy-dev@lists.bx.psu.edu List Subject: Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy? Hi Ann, Configfiles is the way to go. I have writtent the BEAST (and TreeAnnotator), Garli, and RAxML wrappers that are all available in the Galaxy ToolShed. BEAST uses an input xml file that it can parse to execute the analysis. Garli can take a config file that's generated by the Galaxy from the options a user selects in the interface. RAxML is a more traditional command-line application albeit with very convoluted combinations of inputs and outputs that change on every release, which is why my wrapper only supports RAxML 7.3.2. Galaxy provides a lot of choices for handling the applications inputs. MrBayes in this regard is most similar to Garli, so you can take a look at that wrapper. You can take the options from the Galaxy mrbayes interface and write them to a config file that can be fed to MrBayes as a separate NEXUS file just as the Chapter 5 How do I run MrBayes in batch mode? of the MrBayes manual describes. Regards, Alex On Oct 29, 2012, at 2:03 PM, James Taylor ja...@jamestaylor.org wrote: Ann, I think you may be able to do this by generating another nexus file using configfiles in the Galaxy tool config which just contains a command block, similar to the example here: http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes _in_batch_mode.3F -- jt On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann ann.go...@agr.gc.ca wrote: Hello all, I've written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with $ mb and then enter your commands, or directly execute a Nexus file (containing the data and commands) with $ mb nexusfilename. Please correct me if I'm missing something or thinking about this completely wrong. I'd appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.go...@agr.gc.ca Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to remove a broken toolshed install
Hi Greg, We had some occasions where we'd try to install a tool from the toolshed, and it would hang - it appeared that the hg pull was timing out. Was the timeout a regular occurrence? if so, do you know that cause, and were you able to get it resolved? It was repeated, but after a few tries the install would succeed without me really 'resolving' the issue. We haven't run into the issue in a while and I honestly have no idea if this is due to a galaxy upgrade or if we had a temporary run of bad luck with those particular tools. The October 5, 2012 Galaxy distribution news brief includes the following link to information about the process for handling repository installation errors, specifically when the errors occur during cloning. http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy#Handling_repository_installation_errors If you're running an older version of Galaxy, you'll need to update to the October 5 release in order to have these features. The news brief release information is: upgrade: $ hg pull -u -r b5bda7a5c345 Let me know if this is not what you're looking for. Thanks again, this is great. I think we have upgraded past that point now. Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Illumina adaptor sequences in tools - copyright?
Hi all, We are looking at wrapping trimmomatic ( http://www.usadellab.org/cms/index.php?page=trimmomatic ). However to run, it requires the Illumina adaptor sequences, which are copyright. I was wondering if anyone has already dealt with this issue when wrapping other tools and putting them up on a public galaxy instance or in the Toolshed. For instance, I think that FastQC requires the same sequences. I would imagine that Illumina wouldn't want to stop people using these sequences for analysis purposes, but I'm still thinking we might need some sort of permission. Have others dealt with this? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Opinions on organizing tools into repos
Thanks Dannon for adding the Phylogenetics category, I changed the name of this thread, to go in a related by new direction: I wonder if the Galaxy developers and community have any opinions on what is the best way to organize tools into repositories. We've developed a large number of tools to allow my lab to conduct phylogenetic analyses in Galaxy. Inspired by the mothur package in Galaxy, which is all in one repo, I made the decision to add all our related tools to 1 repo on the tool shed. However, it seems that makes individual tools like raxml difficult to find for other users. Recently, we started putting these tools on to bitbucket, and organizing them in different categories (alignment, phylogenetics, orthologies, etc), which is a compromise between all-in-one-repo and each-its-own-repo. The thing is that many of the tools do not stand alone, and really are designed to function with other tools in the package. Any philosophies or opinions are welcome, as I feel like I have not come to a good solution on this... Todd On 10/29/2012 1:50 PM, Dannon Baker wrote: On Oct 29, 2012, at 4:40 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: This is an interesting project. I'm glad to see more people working on phylogenetics related wrappers and workflows. I wonder if we could get a Phylogenetics category added to the main Galaxy Toolshed, so we could put all the relevant wrappers in there to make them easier to find considering the apparent duplication of efforts. Good idea, the main toolshed now has a Phylogenetics category. -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- *** Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA *** Lab Website http://labs.eemb.ucsb.edu/oakley/todd/ Twitter: @UCSB_OakleyLab *Recent Papers: * * Pancrustacean Phylotranscriptomics MBE Paper http://mbe.oxfordjournals.org/content/early/2012/09/12/molbev.mss216.abstract * Convergent Evolution in Cephalopoda BMC Ev Biol http://www.biomedcentral.com/1471-2148/12/129/abstract * Cnidocyte discharge regulated by opsin and light BMC Biology Paper http://tinyurl.com/7dajl2q Scientific American Write-up http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/ * Sponge Larvae Could be Guided by Cryptochrome J Exp Biol. Paper http://jeb.biologists.org/content/215/8/ii | Nature News http://www.nature.com/nature/journal/v484/n7393/full/484145d.html ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] download dataset from the proxy-ed Galaxy failed with broken link
If I downloaded with curl -i, the page it returned was: pwbcad@gamma01:tmp$ curl -i http://galaxy-qa.garvan.unsw.edu.au/datasets/dc097fa4e7ad53f6/display?to_ext=fastqsanger HTTP/1.1 302 Found Date: Tue, 30 Oct 2012 04:25:21 GMT Server: PasteWSGIServer/0.5 Python/2.6.6 content-type: text/html location: /root?dataset_id=dc097fa4e7ad53f6filename=None Set-Cookie: galaxysession=c6ca0ddb55be603a4107d5e4793b9ce28e93ce1e646977c209d1af46a242147b57953de37776fcc2; expires=Mon, 28-Jan-2013 15:25:21 GMT; httponly; Max-Age=7776000; Path=/; Version=1 Vary: Accept-Encoding Transfer-Encoding: chunked html headtitleFound/title/head body h1Found/h1 pThe resource was found at a href=/root?dataset_id=dc097fa4e7ad53f6amp;filename=None/root?dataset_id=dc097fa4e7ad53f6amp;filename=None/a; you should be redirected automatically. !-- --/p hr noshade div align=rightWSGI Server/div /body /html Don't know why the apache returned 302 only when access via wget or curl. Derrick On Sat, Oct 27, 2012 at 7:44 AM, Derrick Lin klin...@gmail.com wrote: Hi Nate, I checked and what downloaded is a webpage, I opened it on browser, and screenshot attached. Basically it displays error saying File not found. But dataset download works fine via browser. Cheers, Derrick On Fri, Oct 26, 2012 at 11:44 PM, Nate Coraor n...@bx.psu.edu wrote: On Oct 24, 2012, at 11:15 PM, Derrick Lin wrote: Hi guys, On our Galaxy is proxy-ed via Apache according to the wiki guide, the normal download dataset via browser is working fine. However, when I tried download from command line via wget or curl -O (I copied the dataset URL by right clicking the floppy disk icon). And here is the wget output: pwbcad@gamma01:tmp$ wget http://galaxy.demo.edu.au/galaxy/datasets/ccc5aff28d2c8616/display?to_ext=fastq --2012-10-25 10:57:42-- http://galaxy.demo.edu.au/galaxy/datasets/ccc5aff28d2c8616/display?to_ext=fastq Resolving galaxy.demo.edu.au... 1xx.x4.1xx.xx5 Connecting to galaxy.demo.edu.au|1xx.x4.1xx.xx5|:80... connected. HTTP request sent, awaiting response... 302 Found Location: /galaxy/root?dataset_id=ccc5aff28d2c8616filename=None [following] --2012-10-25 10:57:42-- http://galaxy.demo.edu.au/galaxy/root?dataset_id=ccc5aff28d2c8616filename=None Connecting to galaxy.demo.edu.au|129.94.136.205|:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: root?dataset_id=ccc5aff28d2c8616filename=None.1 [ = ] 28,476 --.-K/s in 0.001s 2012-10-25 10:57:42 (31.4 MB/s) - root?dataset_id=ccc5aff28d2c8616filename=None.1 saved [28476] It seems like the Apache returned another URL (returned 302, probably due to proxy) and the new URL is broken. Hi Derrick, What are the contents of the file that wget saved? This should give you a clue as to what's going on. --nate Thanks in advance. Cheers, Derrick ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] download dataset from the proxy-ed Galaxy failed with broken link
Hi Ross, Good point and it makes sense in term of security. But I just tried it, and it didn't help. I captured these two from the Paste log (not apache log): xx.xx.1xx.xx - - [30/Oct/2012:15:42:17 +1100] GET /galaxy_dev/datasets/10b866a1b258d1f1/display?to_ext=fastqsanger HTTP/1.1 302 - - Wget/1.12 (linux-gnu) galaxy.web.framework DEBUG 2012-10-30 15:42:17,676 Error: this request returned None from get_history(): http://pwbc.garvan.unsw.edu.au/galaxy_dev/root xx.xx.1xx.xx - - [30/Oct/2012:15:42:17 +1100] GET /galaxy_dev/root?dataset_id=10b866a1b258d1f1filename=None HTTP/1.1 200 - - Wget/1.12 (linux-gnu) Another observation is, I can wget my own dataset from the main Galaxy straight away without providing any credential. Maybe something wrong with my universe ini file. Derrick On Tue, Oct 30, 2012 at 3:32 PM, Ross ross.laza...@gmail.com wrote: That url requires a login from here - have you tried supplying it - eg curl -i -u user:password target On Tue, Oct 30, 2012 at 3:27 PM, Derrick Lin klin...@gmail.com wrote: If I downloaded with curl -i, the page it returned was: pwbcad@gamma01:tmp$ curl -i http://galaxy-qa.garvan.unsw.edu.au/datasets/dc097fa4e7ad53f6/display?to_ext=fastqsanger HTTP/1.1 302 Found Date: Tue, 30 Oct 2012 04:25:21 GMT Server: PasteWSGIServer/0.5 Python/2.6.6 content-type: text/html location: /root?dataset_id=dc097fa4e7ad53f6filename=None Set-Cookie: galaxysession=c6ca0ddb55be603a4107d5e4793b9ce28e93ce1e646977c209d1af46a242147b57953de37776fcc2; expires=Mon, 28-Jan-2013 15:25:21 GMT; httponly; Max-Age=7776000; Path=/; Version=1 Vary: Accept-Encoding Transfer-Encoding: chunked html headtitleFound/title/head body h1Found/h1 pThe resource was found at a href=/root?dataset_id=dc097fa4e7ad53f6amp;filename=None/root?dataset_id=dc097fa4e7ad53f6amp;filename=None/a; you should be redirected automatically. !-- --/p hr noshade div align=rightWSGI Server/div /body /html Don't know why the apache returned 302 only when access via wget or curl. Derrick On Sat, Oct 27, 2012 at 7:44 AM, Derrick Lin klin...@gmail.com wrote: Hi Nate, I checked and what downloaded is a webpage, I opened it on browser, and screenshot attached. Basically it displays error saying File not found. But dataset download works fine via browser. Cheers, Derrick On Fri, Oct 26, 2012 at 11:44 PM, Nate Coraor n...@bx.psu.edu wrote: On Oct 24, 2012, at 11:15 PM, Derrick Lin wrote: Hi guys, On our Galaxy is proxy-ed via Apache according to the wiki guide, the normal download dataset via browser is working fine. However, when I tried download from command line via wget or curl -O (I copied the dataset URL by right clicking the floppy disk icon). And here is the wget output: pwbcad@gamma01:tmp$ wget http://galaxy.demo.edu.au/galaxy/datasets/ccc5aff28d2c8616/display?to_ext=fastq --2012-10-25 10:57:42-- http://galaxy.demo.edu.au/galaxy/datasets/ccc5aff28d2c8616/display?to_ext=fastq Resolving galaxy.demo.edu.au... 1xx.x4.1xx.xx5 Connecting to galaxy.demo.edu.au|1xx.x4.1xx.xx5|:80... connected. HTTP request sent, awaiting response... 302 Found Location: /galaxy/root?dataset_id=ccc5aff28d2c8616filename=None [following] --2012-10-25 10:57:42-- http://galaxy.demo.edu.au/galaxy/root?dataset_id=ccc5aff28d2c8616filename=None Connecting to galaxy.demo.edu.au|129.94.136.205|:80... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: root?dataset_id=ccc5aff28d2c8616filename=None.1 [ = ] 28,476 --.-K/s in 0.001s 2012-10-25 10:57:42 (31.4 MB/s) - root?dataset_id=ccc5aff28d2c8616filename=None.1 saved [28476] It seems like the Apache returned another URL (returned 302, probably due to proxy) and the new URL is broken. Hi Derrick, What are the contents of the file that wget saved? This should give you a clue as to what's going on. --nate Thanks in advance. Cheers, Derrick ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this
Re: [galaxy-dev] download dataset from the proxy-ed Galaxy failed with broken link
On Tue, Oct 30, 2012 at 4:03 PM, Ross ross.laza...@gmail.com wrote: Doesn't make sense that you can wget directly from the paste process if you have security properly configured! That's what you can do with the main Galaxy site. Not sure if that's intentional though. You can try wget --no-check-certificate https://main.g2.bx.psu.edu/datasets/851fbe5b7ff576a6/display?to_ext=tabular See if you can download my own dataset without providing any credential. Do you have Apache authenticating and passing headers through to the paste process - this section in universe_wsgi.ini # User authentication can be delegated to an upstream proxy server (usually # Apache). The upstream proxy should set a REMOTE_USER header in the request. # Enabling remote user disables regular logins. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy use_remote_user = True If so, you should not be able to access anything via the paste process directly without adding authentication headers. Once that's fixed (you do NOT want anyone to be able to do what you can do - it bypasses all security!) the apache configuration will probably need tweaking. It's hard to advise - it's mostly voodoo IMHO - do you have an apache fluent sysadmin? We don't use Apache for authentication. Thus use_remote_user = False. Will read more about this remote user thing. Cheers Derrick ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
