Re: [galaxy-dev] How to redirect output of all the galaxy tools to another directory?
I want to redirect the output. For example the output of tophat2 is stored in ./tophat2 I want to redirect it to my location. On Thu, Feb 14, 2013 at 7:32 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: you can change the location where all the dataset files are stored in universe_wsgi.ini: # Dataset files are stored in this directory. file_path = database/files if this is, what you want? Regards, Hans-Rudolf On 02/14/2013 05:40 AM, Sachit Adhikari wrote: I want to redirect all the output of Galaxy to another directory(actually a external hard drive with full write access). How can I do that? Thanks __**_ 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 redirect output of all the galaxy tools to another directory?
Just realized, you asked this question already. Please see: http://dev.list.galaxyproject.org/Where-is-the-output-of-tools-stored-in-Galaxy-td4657655.html where your question was answered by me and others on the list Regards, Hans-Rudolf On 02/14/2013 09:29 AM, Sachit Adhikari wrote: I want to redirect the output. For example the output of tophat2 is stored in ./tophat2 I want to redirect it to my location. On Thu, Feb 14, 2013 at 7:32 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: you can change the location where all the dataset files are stored in universe_wsgi.ini: # Dataset files are stored in this directory. file_path = database/files if this is, what you want? Regards, Hans-Rudolf On 02/14/2013 05:40 AM, Sachit Adhikari wrote: I want to redirect all the output of Galaxy to another directory(actually a external hard drive with full write access). How can I do that? Thanks _ 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] Datasets linked into Galaxy do not work
Hi Nate, copied datasets do work and I run Galaxy from the server root. Thanks, Sarah - Original Message - From: Nate Coraor n...@bx.psu.edu To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Wednesday, February 13, 2013 8:22:10 PM Subject: Re: [galaxy-dev] Datasets linked into Galaxy do not work On Feb 12, 2013, at 11:17 AM, Sarah Diehl wrote: Hi all, I have problems with datasets that were linked into Galaxy data libraries (as Admin: Add datasets, select Upload files from filesystem paths and Link to files without copying to Galaxy). Those files cannot be looked at, downloaded or viewed in a genome browser. Errors in the browser are: The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this server. The requested URL /library_common/download_dataset_from_folder was not found on this server. An error occurred while accessing: http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam Read error; BinaryCodec in readmode; streamed file (filename not available) I don't see any errors in the log files. We do this kind of linking a lot and everything worked fine in the past. I need to use this feature and need it to work, due to hard disk space and data duplication. Hi Sarah, Do display applications work correctly for datasets that were uploaded to a library and copied in to Galaxy rather than linked? Do you run Galaxy from the server root (http://galaxy.immunbio.mpg.de/) or some path underneath the root? Thanks, --nate Any help is appreciated. Best regards, Sarah ___ 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] changing datasets file_path storage location
Hi Derrick, We did that a year ago, while changing the mount point as part of setting up a shared file system between our Galaxy node and a cluster. Naturally we did a backup first, but I don't recall any issues from this. At the time Nate just advised not to have any jobs running at the time (and stop Galaxy of course). http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-February/008383.html Peter On Thursday, February 14, 2013, Derrick Lin wrote: Hi Shantanu, We are facing the same situation that migrating galaxy dataset to a new location is needed. I am wondering if you have done it successfully? Would be nice if you can share your experience with us. Cheers, D On Fri, Nov 30, 2012 at 9:21 AM, Shantanu Pavgi (Campus) pa...@uab.eduwrote: We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we should be considering before making this change. There are certain fields in the database (e.g. command_line in jobs table) which contain absolute path of datasets. Do we need to update any of these fields to make sure Galaxy is functional after file_path is changed? -- Thanks, Shantanu ___ 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] Bug in Galaxy Reports tool
Hhhmm seems to behave normally in our running (latest) dist release 8530:a4113cc1cb5e tip Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: dinsdag 12 februari 2013 12:29 Aan: joachim.ja...@vib.be CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Bug in Galaxy Reports tool Hello joachim, Thanks for reporting this. I've added a Trello card for this issue: https://trello.com/card/galaxy-reports/506338ce32ae458f6d15e4b3/610 Greg Von Kuster On Feb 12, 2013, at 6:05 AM, Joachim Jacob |VIB| wrote: Hi all, Running ~/galaxy-dist/run_reports.sh brings up the Galaxy Reports interface on poort 9001. When clicking on 'Jobs per user' - picking a user - picking a month - and clicking on 'State' in the bar at the top, clears the screen. Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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] hg19 reference gnome for Tophat2
I tried with many data but still the same problem and regarding settings I haven't changed a thing of Tophat2. What might be causing this error? Thanks On Wed, Feb 13, 2013 at 7:10 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: If the other outputs are fine, then the problem is likely with your data and/or your Tophat settings. Good luck, J. On Feb 13, 2013, at 8:22 AM, Sachit Adhikari wrote: Ok sorry. I did that, but the output of splice junctions is empty. The other outputs looks fine. What might be the problem? Thanks, Sachit On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Shall I replace: /orig/path/hg19hg19hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Yes, that's correct. Finally, please email only galaxy-dev with questions about local installations; galaxy-user is for questions about how to use Galaxy. 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/
Re: [galaxy-dev] Changing job command line.
Hi Nate, Thanks for your reply, I guess the idea is that the job is prepared in the interface which lets a user select the grid. This is currently located in my galaxy instance as a if statement in the default job dispatcher. Just before it sends it to the job runner and all the preparation is done there. But regarding the command line you are probably right, it would just mean that every job runner on our instance will have to be patched to include this if statement as to whether the command line needs to be reassigned. Another simple question regarding adding UI options to toolform.mako. Could i parse them to my module using javascript. Although I feel the best approach would be to add these options to the job model and then they would remain tracked in the database. Cheers James. On 2/14/2013 4:20 AM, Nate Coraor wrote: On Feb 4, 2013, at 6:03 PM, James Boocock wrote: Hi All, I am currently working on a clustering interface for galaxy that will hopefully enable users to pick the grid in the tool form. With tools that need access to files within the galaxy directory, I have an idea to create a symlinked fake galaxy root with all the files the tools needs for galaxy. This is done currently in my own xml format for each grid. Problem is when parsing a tool_wrapper variable I need to prepare the job and add my additional commands to the command line so that the fake galaxy dir is created with the symlinked databases. Is it bad practice to disable preparation in each tool runner if the job has come from my clustering module or is there a better way to do this. Will the job runners wrapper.prepare() overwrite any of my changes to the command-line when the job makes its way to the runner say local.py. Hi James, You'll probably need to make the changes to the command line after the command line has been assembled in prepare(). Can you do this later in prepare()? --nate Cheers James. ___ 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] hg19 reference gnome for Tophat2
Try using the Tophat test data to verify your installation; it's known to have splice junctions: http://tophat.cbcb.umd.edu/tutorial.html http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz Good luck, J. On Feb 14, 2013, at 6:29 AM, Sachit Adhikari wrote: I tried with many data but still the same problem and regarding settings I haven't changed a thing of Tophat2. What might be causing this error? Thanks On Wed, Feb 13, 2013 at 7:10 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: If the other outputs are fine, then the problem is likely with your data and/or your Tophat settings. Good luck, J. On Feb 13, 2013, at 8:22 AM, Sachit Adhikari wrote: Ok sorry. I did that, but the output of splice junctions is empty. The other outputs looks fine. What might be the problem? Thanks, Sachit On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: Shall I replace: /orig/path/hg19hg19hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Yes, that's correct. Finally, please email only galaxy-dev with questions about local installations; galaxy-user is for questions about how to use Galaxy. 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/
Re: [galaxy-dev] Error with local toolshed and remote user authentication: HTTPError: HTTP Error 401: Authorization Required
On Feb 13, 2013, at 3:25 PM, Carlos Borroto wrote: On Wed, Feb 13, 2013 at 3:10 PM, Greg Von Kuster g...@bx.psu.edu wrote: Carlos, Sorry you're having difficulty here. I'm not able to help very much here because I'm not familiar with the Galaxy remote user authentication process and I don't have an environment in which to mess with it. In case it helps, however, the Tool Shed uses the same code for remote user authentication as Galaxy does, so if you have gotten this to work for a Galaxy instance, you should be able to use the same configuration for the Tool Shed. Hi Greg, Maybe I should explain myself better here and also create a trello card to check progress on this issue. When you activate use_remote_user in the Tool Shed and correctly configure your web server(ex. Apache), everything will work as in Galaxy. You will get presented with an Apache basic authentication box and you will get access Tool Shed as expected. Every single feature in the Tool Shed works perfectly as far as I can tell. Where is the problem them?. Well, it is when you try to install a tool from the Tool Shed in a Galaxy instance. When Galaxy tries to clone the mercurial repository from the Tool Shed it gets a HTTP/1.1 403. Even so if you made sure Apache will allow unrestricted access from the Galaxy host. You still get HTTP/1.1 403 from the Tool Shed, as the Tools Shed is expecting a remote user header the Galaxy instance is not providing. I'm not so sure what is the best way to approach this issue. I see two possibilities thou. Galaxy will have to provide a remote user header, maybe assume the Galaxy user is the same as the Tool Shed, a good guess I think, or the Tool Shed would have to allow access to /repositories/ even if there is no a remote user in the header. Again, I don't know if either of these options are technically possible or safe to use. Hi Carlos, You may be able to get this to work by setting 'display_servers = galaxy_server_hostname' in your community_wsgi.ini file. This instructs Galaxy's remote user middleware to allow connections from this host even if a remote user has not been provided. It looks like all the pieces are there in the Tool Shed to make it work. --nate Thanks for looking into this, Carlos ___ 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] Reloading a tools configuration does not seem to actually work
On Feb 13, 2013, at 5:56 PM, Anthonius deBoer wrote: Interesting! But maybe it is not the manager that is the bottleneck, but which process is the one that takes the inputs from the webpage (or in the API) and prepares all the files that are produced by the workflows? I guess it is the MAIN server? THAT is the one that is the bottleneck I think then... Are there any plans to make that process parallel? Well, you can run as many web servers as you'd like, which should help to alleviate this problem. Whichever server happens to be doing the work will be slow, but the rest should be unaffected. What I am facing, is that I have 100 FASTQ pairs or so, for a single flowcell, I can start the analysis of that set from the UI, but it will just crank through them and takes about 2-4 minutues for each pair to be processed, so with 100 pairs or so, you are looking 3-4 hours of an hourglass before control is given back to the user... Is this in the context of starting a workflow with hundreds of inputs? --nate It would be ideal if we would farm out the parsing of the web input to the cluster, so the creation of the histories and datasets is no longer the bottleneck How do others deal with large sequencing projects on this list? Are there any groups that routinely do 100-200 pairs of FASTQ files from within galaxy? I would like to hear their experience... Thanks Thon On Feb 13, 2013, at 01:44 PM, Nate Coraor n...@bx.psu.edu wrote: On Feb 13, 2013, at 4:12 PM, Anthonius deBoer wrote: Would this problem go away if I only used ONE webserver in my proxy setting and not use a balancer? I may not need it and if it means I could not use the toolshed effectively, it may be worth it not to use balancing.. No, because your manager/handlers will still need to be restarted to pick up the new tools. The only way you can have it work without restarting is to have everything in a single process. What i really need is the manager being balanced, since submitting a workflow with 100's of BAM files can take hours just to get started...ANy change we can run multiple managers? I'm surprised the manager is the holdup here since all it does is assign a handler. Regardless, in the development branch (which will be the next stable/release branch), the manager has been killed, and handlers are assigned directly by the web processes. --nate Thanks On Feb 13, 2013, at 07:59 AM, Nate Coraor n...@bx.psu.edu wrote: On Feb 7, 2013, at 2:43 PM, Anthonius deBoer wrote: That's very unfortunate... I have a ton of tools and I guess now I have to create a package for them in a local toolshed to update them in a running galaxy server? In any case...The toolshed installation also does not work for me...I still have to restart galaxy, even after using the toolshed approach to install a tool...It either does not show up at all or give a bunch of errors, about not being able to find the tool... Is this also related to the fact I have two webservers and am behind a proxy server as well? Hi Thon, Essentially yes, there is no way for one web process to communicate with others that it has installed a tool. We'd like to allow for this sort of notification via a message queue, but we don't have a proper message queue in Galaxy right now. --nate Thon On Feb 07, 2013, at 05:29 AM, Dannon Baker dannonba...@me.com wrote: Unfortunately not, and with the migration of tools to the toolshed installation mechanism I don't imagine this will be addressed (at least by the team) anytime soon. If you wanted you could probably write a script that would reload a specified tool in each of the separate web processes, or just implement a complete rolling restart of your web processes to avoid service disruption while still loading the tool updates. -Dannon On Feb 6, 2013, at 8:40 PM, Anthonius deBoer thondeb...@me.com wrote: I am indeed using multiple web processes and I guess I am talking about the old admine tool reloader... Is there any other way to do this for your own tools that you just manually place in tools etc.? Thon On Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote: Are you using multiple web processes, and are you referring to the old admin tool reloader or the toolshed reloading interface? -Dannon On Feb 5, 2013, at 9:13 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I find that reloading a tool's configuration file does not really work. First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)... But when I try to run my tool, the old bug is still there... I am using proxy server so something may still be
Re: [galaxy-dev] Problems linking Data inside Galaxy
On Feb 13, 2013, at 6:42 PM, Gaueko Erge wrote: Hi Nate, Thank you for your reply. After a lot of trying I was able to figure this out Entries in my alignsec.loc file were pointing to: seq AaegL1 /db/galaxydb/AaegL1/seq/ seq AgamP3 /db/galaxydb/AgamP3/seq/ and not to: seq AaegL1 /db/galaxydb/AaegL1/seq/AaegL1.2bit seq AgamP3 /db/galaxydb/AgamP3/seq/AgamP3.2bit As required for this this work I guess, I was confused and/or did not understand the instructions well. Also, I was confused because I thought that the '2bit' files had to be present in the 'twobit.loc' file and not in alignsec.loc Honestly, I am still trying to mentally sort out what datasets are used by ucsc browser (local installation) and what datasets are used only by galaxy. AND how to proceed to upload my own genomes to both galaxy and to my local deployment of ucsc browser Hi Gaueko, I'm glad to hear it's working. If you have any suggestions on how to improve our documentation for this, please let us know. --nate Thanks --G On Wed, Feb 13, 2013 at 1:27 PM, Nate Coraor n...@bx.psu.edu wrote: On Feb 12, 2013, at 10:49 AM, Gaueko Erge wrote: Hi, I have followed, carefully, the instructions posted in:http://wiki.galaxyproject.org/Admin/Data%20Integration Yet, despite my best efforts when I get, say all exons from hg19 build and try to their fetch sequences, galaxy tells me that the sequences for hg19 are not there I find this surprising because I have downloaded: rsync://datacache.g2.bx.psu.edu/indexes/ rsync://hgdownload.cse.ucsc.edu/gbdb/ rsync://hgdownload.cse.ucsc.edu/goldenPath/vicPac1/bigZips databases and added the correct paths to the 'alignseq.loc' file Hi Gaueko, It'd be helpful if you could provide us with the entry from your alignseq.loc file. Also, you may want to verify that your alignseq.loc contains only tabs between the fields, not spaces. --nate Any ideas will be appreciated Thanks --G ___ 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] Reloading a tools configuration does not seem to actually work
On Thu, Feb 14, 2013 at 10:40 AM, Nate Coraor n...@bx.psu.edu wrote: What I am facing, is that I have 100 FASTQ pairs or so, for a single flowcell, I can start the analysis of that set from the UI, but it will just crank through them and takes about 2-4 minutues for each pair to be processed, so with 100 pairs or so, you are looking 3-4 hours of an hourglass before control is given back to the user... Is this in the context of starting a workflow with hundreds of inputs? I believe this is entirely in the web process, creating a workflow requires creating tons of datasets, which requires tons of database flushes. I have a patch to fix this from a long time ago but it would need substantial testing. I think we should also background the process, but this depends on having a way to attach the workflow invocation to the history, hence dataset groups. All the pieces are coming together on this. -- James Taylor, Assistant Professor, Biology/CS, Emory University ___ 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] New release : display problem
Hi, Thanks for the answer. It is after the new galaxy-dist release and if a type is affected, all its children types are too. For example the tabular but that's not the only one. It's is not a question of size I think because very small datasets are not displayed neither. Cheers, Mathieu - Mail original - De: Dannon Baker dannon.ba...@gmail.com À: Mathieu Bahin mathieu.ba...@irisa.fr Cc: galaxy-dev@lists.bx.psu.edu Envoyé: Jeudi 14 Février 2013 00:55:46 Objet: Re: [galaxy-dev] New release : display problem Mathieu, To clarify -- is this after the new galaxy-dist release, or new code in galaxy-central? And, is this *any* tabular file? Or just ones of a particular size? (Files of 50 columns are handled as a special case, for instance) -Dannon On Wed, Feb 13, 2013 at 11:29 AM, Mathieu Bahin mathieu.ba...@irisa.fr wrote: Hi there, I am using my own Galaxy instance and since I updated, I can't see file of several datatypes (for example the 'tabular') clicking on the eye icon. Is that a problem linked to the new release ? Cheers, Mathieu Bahin ___ 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] Environment variables reset after manually restarting Galaxy
Hi Nate, I am sorry I missed your reply... Thanks for your input, will try this soon. Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/13/2013 06:31 PM, Nate Coraor wrote: On Feb 11, 2013, at 7:48 AM, Joachim Jacob |VIB| wrote: Hello all, After a *reboot* of our Galaxy server, the environment variables are set correctly. However, after *restarting* the Galaxy process on a running server, by logging in as Galaxy and running the init script on CentOS as service galaxyd restart, the environment variables seems to be messed up Hi Joachim, It seems odd you'd be logging in as Galaxy to restart the process. Since the system is going to run the init script as root, you should do this as well when you restart it. Presumably whatever init script you are using is properly switching to the galaxy user to start the server process(es). --nate After this manual Galaxy restart, some tools are not found, apparently caused by a modification of the environment variable PATH. Can somebody provide me perhaps with insight on what is causing this, and how to avoid this? My environment variables are set in /etc/profile.d/galaxy_environment_setup (which is a symbolic link to - /home/galaxy/environment_setup ) Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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] New release : display problem
Could you share with me a file that reproduces this behavior? I'm unable to do so on a fresh -dist clone after trying various files and file types. Do you see any errors in the console or galaxy log when this happens? On Thu, Feb 14, 2013 at 2:34 AM, Mathieu Bahin mathieu.ba...@irisa.fr wrote: Hi, Thanks for the answer. It is after the new galaxy-dist release and if a type is affected, all its children types are too. For example the tabular but that's not the only one. It's is not a question of size I think because very small datasets are not displayed neither. Cheers, Mathieu De: Dannon Baker dannon.ba...@gmail.com À: Mathieu Bahin mathieu.ba...@irisa.fr Cc: galaxy-dev@lists.bx.psu.edu Envoyé: Jeudi 14 Février 2013 00:55:46 Objet: Re: [galaxy-dev] New release : display problem Mathieu, To clarify -- is this after the new galaxy-dist release, or new code in galaxy-central? And, is this *any* tabular file? Or just ones of a particular size? (Files of 50 columns are handled as a special case, for instance) -Dannon On Wed, Feb 13, 2013 at 11:29 AM, Mathieu Bahin mathieu.ba...@irisa.fr wrote: Hi there, I am using my own Galaxy instance and since I updated, I can't see file of several datatypes (for example the 'tabular') clicking on the eye icon. Is that a problem linked to the new release ? Cheers, Mathieu Bahin ___ 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] jobs don't get killed when histories deleted?
Hi all, I've created Trello cards for both of these issues: https://trello.com/card/jobs-stop-jobs-on-history-deletion/506338ce32ae458f6d15e4b3/626 https://trello.com/card/jobs-stop-job-function-in-jobs-admin-interface-is-broken/506338ce32ae458f6d15e4b3/627 --nate On Feb 14, 2013, at 2:58 AM, Hans-Rudolf Hotz wrote: Hi Thon I can't help you killing the job on the clusterbut regarding the admin section (and the database): On very rare occasions, we do have jobs (which are not running anymore) but are labelled as running on the Manage jobs page in the admin section. Using the Stop Jobs option does not work to remove them. So I manually change the state to error in the 'job' table, eg: update job set state='error' where id=12345; As always, be very careful when you directly access the MySQL or PostgreSQL database! Regards, Hans-Rudolf On 02/13/2013 09:14 PM, Anthonius deBoer wrote: Hi, I am continue to struggle with the proccess of killing jobs that run on the SGE cluster when deleting histories. I would assume that jobs get removed from the queue when a history they are part of is deleted but in most cases, the jobs stay on the cluster and are not killed I also never have been able to get the kill jobs in the admin section to work (using the 8-Feb version)...It just sites there, returns and the jobs are still there on the cluster and still there in the database Is there anything in the database I can do to really kick out those jobs? Thanks Thon ___ 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/
[galaxy-dev] Datatype display_in_upload not respected in upload1
Hi all, I noticed that when I go in Get Data - Upload File from your computer (i.e. upload1 tool) the File Format list contains also datatypes which have display_in_upload=false in datatypes_conf.xml (e.g. afg, fli), while the list does not contain datatypes which have no display_in_upload attribute at all (e.g. bedstrict, bed6). This sounds like a bug to me, but I have not found any reference around. Thanks, Nicola -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ ___ 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 with local toolshed and remote user authentication: HTTPError: HTTP Error 401: Authorization Required
On Thu, Feb 14, 2013 at 10:30 AM, Nate Coraor n...@bx.psu.edu wrote: You may be able to get this to work by setting 'display_servers = galaxy_server_hostname' in your community_wsgi.ini file. This instructs Galaxy's remote user middleware to allow connections from this host even if a remote user has not been provided. It looks like all the pieces are there in the Tool Shed to make it work. Yes, this did it!. Thanks. ___ 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] Why are the search options in datasets no longer using AND logic?
This is a bug, and it's been fixed in this changeset: https://bitbucket.org/galaxy/galaxy-central/commits/db08c095de0c249f3a6cde62f254c104de1fb6ea Thanks for pointing it out, J. On Feb 13, 2013, at 8:25 PM, Anthonius deBoer wrote: Hi, One very cool feature was to be able to search quickly for datasets using the search feature. You could continue to add terms until your search results in the correct set... It was basically doing an AND search for the terms you entered. This feature has seem to have disappeared? Now a search term replaces your previous term so you can no longer pair your search down and there does not seem to be any support for using AND or Is this a bug or a new feature? Thanks Thon ___ 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] New release : display problem
On Thu, Feb 14, 2013 at 11:01 AM, Dannon Baker dannon.ba...@gmail.com wrote: Could you share with me a file that reproduces this behavior? I'm unable to do so on a fresh -dist clone after trying various files and file types. Do you see any errors in the console or galaxy log when this happens? I'm seeing the same behavior when using Chrome but no when using Firefox. Just in case I deleted all cookies related to galaxy in Chrome and that didn't fix the problem this time. I don't see any errors in paster.log when this happens. Regards, Carlos ___ 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] History does not automatically update anymore
Hi,I have noticed that in the latest version of galaxy-dist, my history does not automatically update anymore.I have to press the refresh circle to have it update...I did change my proxy setup a little, so it would no longer require API calls to be authenticated, while access through the frontend would still require that so it may have something to do with that, but just wanted to check if others see this issue...I will send out my proxy settings in a later email, since it may help people that are struggling with the same...Thon ___ 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] Setting up a proxy with authentication while waiving this for API calls
Hi,I have been struggling with setting up my galaxy system to allow it to use the LDAP authentication for users that come in through the frontend, while not wanting to have to use authentication when user want to access through the APII found some solution and I thought I'd share it with the world so that people may learn from this and maybe also tell me if I am doing something wrong, or worse, insecure!I setup two web servers in the universe file at localhost:8080 and localhost:8081.For the one at 8080 i require authentication, for the one at 8081 I do not in the settings for apache proxy server shown belowThe I setup a ReWriteRule for anything addressed to /api/ and route that to the one at 8081, that does not require authentication, while everything else goes through 8080 which does...It seems to work nicely, although I have a nagging feeling this leaves open some backdoors somewhere, but please tell me if I do...codeDirectory /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static Options FollowSymLinks Order Allow,Deny Allow from all/DirectoryProxy http://localhost:8080AuthType BasicAuthName "GALAXY@GHI. Please log in with your Windows account"AuthBasicProvider ldapAuthLDAPURL "ldap://__YOUR_LDAP_SERVER/ou=Users - Employees,dc=genomichealth,dc=com?sAMAccountName?sub?(objectClass=*)"AuthzLDAPAuthoritative offAuthLDAPBindDN __USERNAME__AuthLDAPBindPassword __PASSWORDRequire valid-userRequestHeader set REMOTE_USER %{AUTHENTICATE_SAMACCOUNTNAME}e/Proxy#Extended the timeout since some GALAXY actions can take a long timeTimeOut 6RewriteEngine onReWriteRule ^(/api/.*) http://localhost:8081$1 [L]RewriteRule ^/static/style/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]RewriteRule ^/static/scripts/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/scripts/packed/$1 [L]RewriteRule ^/static/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/$1 [L]RewriteRule ^/favicon.ico /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/favicon.ico [L]RewriteRule ^/robots.txt /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/robots.txt [L]RewriteRule ^/admin/jobs(.*) http://localhost:8079/admin/jobs$1 [P]RewriteRule ^(.*) http://localhost:8080$1 [P]/codeThon___
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[galaxy-dev] Install NGSRich in local galaxy
HI, Does anyone know who to install NGSRich software on a local instance of Galaxy? I tried to install it from the shed_tool but it does not show up in the repository, so I manually downloaded it from http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=nameoperation=view_or_manage_repositorypage=1async=falseshow_item_checkboxes=falsef-free-text-search=ngsid=feaea37bb0f3bdca But now, I am not sure how to add it into my galaxy env. Any help will be highly appreciated ... Regards, ___ 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] Install NGSRich in local galaxy
Hello Hakeem, Here is a link to the tool shed wiki sections that provide all of the details for installing repositories from the tool shed into your local Galaxy instance. http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance We advise that you use the automatic installation process when installing into your Galaxy instance and not the manual installation process. Greg Von Kuster On Feb 14, 2013, at 5:48 PM, Hakeem Almabrazi wrote: HI, Does anyone know who to install NGSRich software on a local instance of Galaxy? I tried to install it from the shed_tool but it does not show up in the repository, so I manually downloaded it from http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=nameoperation=view_or_manage_repositorypage=1async=falseshow_item_checkboxes=falsef-free-text-search=ngsid=feaea37bb0f3bdca But now, I am not sure how to add it into my galaxy env. Any help will be highly appreciated … Regards, ___ 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/
[galaxy-dev] can't run instance for CloudMan
Hi, I am having a problem with running galaxy on the Amazon cloud. I have tried this several times over the past few days, I followed the list and it seems my instance is up and running. However, when I type the DNS in any browser it can't connect to it. I am kind of aiming in the dark now because I don't know where the problem is, anyone can help? thanks! stefano ___ 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] Setting up a proxy with authentication while waiving this for API calls
There was a small, but important error in the proxy configuration...I had to pass the /api/ part to a proxy again with a [P] directive, not just the [L].So the correct proxy definition is:Directory /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static Options FollowSymLinks Order Allow,Deny Allow from all/DirectoryProxy http://localhost:8080AuthType BasicAuthName "GALAXY@GHI. Please log in with your Windows account"AuthBasicProvider ldapAuthLDAPURL "ldap://__YOUR_LDAP_SERVER/ou=Users - Employees,dc=genomichealth,dc=com?sAMAccountName?sub?(objectClass=*)"AuthzLDAPAuthoritative offAuthLDAPBindDN __USERNAME__AuthLDAPBindPassword __PASSWORDRequire valid-userRequestHeader set REMOTE_USER %{AUTHENTICATE_SAMACCOUNTNAME}e/Proxy#Extended the timeout since some GALAXY actions can take a long timeTimeOut 6RewriteEngine onReWriteRule ^(/api/.*) http://localhost:8081$1 [P,L]RewriteRule ^/static/style/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]RewriteRule ^/static/scripts/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/scripts/packed/$1 [L]RewriteRule ^/static/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/$1 [L]RewriteRule ^/favicon.ico /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/favicon.ico [L]RewriteRule ^/robots.txt /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/robots.txt [L]RewriteRule ^/admin/jobs(.*) http://localhost:8079/admin/jobs$1 [P]RewriteRule ^(.*) http://localhost:8080$1 [P]On Feb 14, 2013, at 02:41 PM, Anthonius deBoer thondeb...@me.com wrote:Hi,I have been struggling with setting up my galaxy system to allow it to use the LDAP authentication for users that come in through the frontend, while not wanting to have to use authentication when user want to access through the APII found some solution and I thought I'd share it with the world so that people may learn from this and maybe also tell me if I am doing something wrong, or worse, insecure!I setup two web servers in the universe file at localhost:8080 and localhost:8081.For the one at 8080 i require authentication, for the one at 8081 I do not in the settings for apache proxy server shown belowThe I setup a ReWriteRule for anything addressed to /api/ and route that to the one at 8081, that does not require authentication, while everything else goes through 8080 which does...It seems to work nicely, although I have a nagging feeling this leaves open some backdoors somewhere, but please tell me if I do...codeDirectory /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static Options FollowSymLinks Order Allow,Deny Allow from all/DirectoryProxy http://localhost:8080AuthType BasicAuthName "GALAXY@GHI. Please log in with your Windows account"AuthBasicProvider ldapAuthLDAPURL "ldap://__YOUR_LDAP_SERVER/ou=Users - Employees,dc=genomichealth,dc=com?sAMAccountName?sub?(objectClass=*)"AuthzLDAPAuthoritative offAuthLDAPBindDN __USERNAME__AuthLDAPBindPassword __PASSWORDRequire valid-userRequestHeader set REMOTE_USER %{AUTHENTICATE_SAMACCOUNTNAME}e/Proxy#Extended the timeout since some GALAXY actions can take a long timeTimeOut 6RewriteEngine onReWriteRule ^(/api/.*) http://localhost:8081$1 [L]RewriteRule ^/static/style/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]RewriteRule ^/static/scripts/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/scripts/packed/$1 [L]RewriteRule ^/static/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/$1 [L]RewriteRule ^/favicon.ico /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/favicon.ico [L]RewriteRule ^/robots.txt /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/robots.txt [L]RewriteRule ^/admin/jobs(.*) http://localhost:8079/admin/jobs$1 [P]RewriteRule ^(.*) http://localhost:8080$1 [P]/codeThon___ 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/___
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Re: [galaxy-dev] Bug in Galaxy Reports tool
Hhhmmm.. and now it doesn't and reproduces what Joachim reported... -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: donderdag 14 februari 2013 11:45 Aan: Greg Von Kuster; joachim.ja...@vib.be CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Bug in Galaxy Reports tool Hhhmm seems to behave normally in our running (latest) dist release 8530:a4113cc1cb5e tip Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: dinsdag 12 februari 2013 12:29 Aan: joachim.ja...@vib.be CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Bug in Galaxy Reports tool Hello joachim, Thanks for reporting this. I've added a Trello card for this issue: https://trello.com/card/galaxy-reports/506338ce32ae458f6d15e4b3/610 Greg Von Kuster On Feb 12, 2013, at 6:05 AM, Joachim Jacob |VIB| wrote: Hi all, Running ~/galaxy-dist/run_reports.sh brings up the Galaxy Reports interface on poort 9001. When clicking on 'Jobs per user' - picking a user - picking a month - and clicking on 'State' in the bar at the top, clears the screen. Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/ ___ 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] History does not automatically update anymore
I do now actually get an error message in my browser saying Error getting history updates from the server. Internal Server Error Any ideas? I suspect it is my proxy server settings but not sure. Thon From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Anthonius deBoer Sent: Thursday, February 14, 2013 2:31 PM To: Galaxy-dev Galaxy-dev Subject: [galaxy-dev] History does not automatically update anymore Hi, I have noticed that in the latest version of galaxy-dist, my history does not automatically update anymore. I have to press the refresh circle to have it update... I did change my proxy setup a little, so it would no longer require API calls to be authenticated, while access through the frontend would still require that so it may have something to do with that, but just wanted to check if others see this issue... I will send out my proxy settings in a later email, since it may help people that are struggling with the same... Thon image001.png___ 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] History does not automatically update anymore
Aaanndd ofcourse it was due to the proxy settings. I noticed that the history refresh is done through a call of the API and since I had re-routed that to a different web server than the main server, it broke. But once I added this rewrite rule: ReWriteRule ^(/api/histories/.*) http://localhost:8080$1 [P,L] Before the other /api/ one, the refresh of the history worked again. It seems I need to spend a little more time on this whole proxy setting thing. Thon From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de Boer Sent: Thursday, February 14, 2013 10:58 PM To: 'Galaxy-dev Galaxy-dev' Subject: Re: [galaxy-dev] History does not automatically update anymore I do now actually get an error message in my browser saying Error getting history updates from the server. Internal Server Error Any ideas? I suspect it is my proxy server settings but not sure. Thon From: galaxy-dev-boun...@lists.bx.psu.edu mailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Anthonius deBoer Sent: Thursday, February 14, 2013 2:31 PM To: Galaxy-dev Galaxy-dev Subject: [galaxy-dev] History does not automatically update anymore Hi, I have noticed that in the latest version of galaxy-dist, my history does not automatically update anymore. I have to press the refresh circle to have it update... I did change my proxy setup a little, so it would no longer require API calls to be authenticated, while access through the frontend would still require that so it may have something to do with that, but just wanted to check if others see this issue... I will send out my proxy settings in a later email, since it may help people that are struggling with the same... Thon image001.png___ 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/
