Re: [galaxy-dev] Patch for RepeatMasker.xml for RepeatMasker 3.3.0
Hi Simon, thank you for your contribution. I updated the toolshed version to 0.1.1 with your changes. Ciao! Bjoern Dear Galaxians, We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is the expected version, as I can't find any statement about what is required in the Galaxy tool dependencies for RepeatMasker. Anyway, when a job is submitted with no repeats, RepeatMasker 3.3.0 doesn't create the various output and summary files (.tbl, .out.gff, .out.html, .masked). This causes the Galaxy job to fail with an error message that scares the end user. I attach a patch to handle this case, by touch'ing these files before trying to copy them. Now such jobs succeed with empty output. I think this is clearer, and certainly less scary. Is there a better mechanism for me to contribute such fixes other than posting patches on this list? cheers, Simon === Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. === ___ 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 do I allow a large group of users to RUN my workflow without them having to make a local copy
Thon: You can share a workflow through a URL, which you can send to all members of the group. anton Anton Nekrutenko http://www.galaxyproject.org On Jan 31, 2013, at 10:52 PM, Anthonius deBoer wrote: Hi, I am trying to build some workflows for people that are part of a group and I want to share that workflow with them, so that they can run the workflow without having to make a local copy for them self. It seems I can only share a workflow in that manner with an individual, and not with a group... Am I reading that correctly? It seems strange not to be able to share workflows with groups if you can share them with individual users.. I also have to know the exact username (email) for each user, rather than being able to choose it from a list... Is there any reason for this or is just underdeveloped? 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/
[galaxy-dev] install Galaxy in Windows (URGENT)
Hi, I have Windows Vista and 8 in two separate laptops. I need to install a local version of Galaxy server in both the systems. I am unable to understand or follow the instructions given in your website (http://wiki.galaxyproject.org/Admin/Get%20Galaxy). Could you kindly help me or just explain me stepwise how to install it in my system? Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK ___ 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 Galaxy in Windows (URGENT)
On Fri, Feb 1, 2013 at 2:33 PM, Prasun Dutta prasundutt...@yahoo.co.in wrote: Hi, I have Windows Vista and 8 in two separate laptops. I need to install a local version of Galaxy server in both the systems. I am unable to understand or follow the instructions given in your website (http://wiki.galaxyproject.org/Admin/Get%20Galaxy). Could you kindly help me or just explain me stepwise how to install it in my system? Regards, Prasun Dutta Quoting that page, The installation procedure is simple and is nearly identical for UNIX/Linux and Mac OS X. We are no longer supporting the Windows platform with our distribution, so you will have to build your own Python eggs if you want to install it on Windows (see Admin/Config/Windows for some tips). Of course, Windows users can use our public Galaxy server from their browsers. Right now you *can't* install Galaxy on Windows. Only if you were an experienced Python developer with cross-platform experience would it even be worth trying. The idea is you just run a web-browser on your (Windows) Laptop, and connect to Galaxy running on a (Linux) server. Just like you should be able to use your (Windows) Laptop to connect to the public Galaxy at http://usegalaxy.org Peter ___ 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 reference genome Bwa and Bowtie!
Hi Hakeem, The set up for samtools looks correct. If the problems that you had with BWA/Bowtie were due to an error in our wiki, please send in the suggested changes to me. We want this to be correct. For the SAM-BAM tool - in the UI, there will never be a list of genomes - that is not one of the form options. This tool either interprets the database assigned to the input dataset (option Choose the source for the reference list: Locally cashed) or allows the user to select a genome custom reference genome (option same, but History). So, to give this a test, run a dataset through it that has hg19 assigned as the reference and examine the results. If you are curious about custom genomes, which are used as fasta file datasets from a user's history with tools (instead of installed reference genomes), more is here: http://wiki.galaxyproject.org/Support#Custom_reference_genome Take care, Jen Galaxy team On 2/1/13 6:40 AM, Hakeem Almabrazi wrote: Thank you Jennifer for your help. I already resolved the issues with Bwa and Bowtie. I was misled with some missing instructions but I managed to resolved them by searching online. Now I am stuck at the SAM Tools displaying a reference genome :)... I will give more details at what I am doing hopefully someone can help. My reference fasta (hg10.fasta) file is located at (/usr/local/galaxy_data/hg19/samtools/) I ran the following command to build the samtools index file samtools faidx hg19.fasta This generated the hg19.fasta.fai Here is the content of the above path after running the samtools indexing command: -rwxr-xr-x 1 galaxy galaxy hg19.fasta -rw-rw-r-- 1 galaxy galaxy hg19.fasta.fai For my ~tool-data/sam_fa_indices.loc file here is the info I am using to reference the index file: IndexTABhg19TAB/usr/local/galaxy_data/hg19/samtools/hg19.fasta ### I restarted my server but I do not see anything when I go to GUI-NGS:SamTools-Sam-To-Bam-Choose the source for the reference list:HISTORY Is there something I am missing or is there anything else I need to change at this point. Regards, -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Thursday, January 31, 2013 6:45 PM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie! Hello Hakeem, It is difficult to troubleshoot without knowing all the exact details of your configuration, but it sounds as if you are on the right path and the last few bits should be easy to reconcile with our documentation. In particular, check that the builds.txt file contains the genomes that you are adding. Also, if you want to view or use our indexes (if we have them available for your genome), or just want to double check your indexes vs ours, the rsync service can be used. Both are described in this wiki: http://wiki.galaxyproject.org/Admin/Data%20Integration I am not sure that I understand step #5, but there is another confusing point here. You want the data and all tools under the primary Galaxy directory hierarchy or have the alternate locations specified in the universe config file. Also, it is important to not us symbolic paths in the .loc files - use the full hard path to the indexed data. Hopefully this helps! If you do need more feedback, please be sure to leave the mailing list on the cc to help us track any reply, Best, Jen Galaxy team On 1/30/13 4:19 PM, Hakeem Almabrazi wrote: Hi, I just installed Galaxy in local Centos Vm. I did my best to get everything working ( I think). I followed the instructions in this Wiki (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) to install reference genomes for the tools Bwa and Bowtie. Here is what I did in details: 1.I installed all the software and added them to the PATH and everything seems to be working. 2.Then I created the indices as explained. 3.I put all the indices in the same recommended directory structure and gave all access rights to the Galaxy user which runs the Galaxy server. 4.I created the loc files (bowtie_indices.loc and bowtie_indices_color.loc and bwa_index.loc) and populate them with the recommended contents) and place them in ~/tool_data/ folder. 5.I copied the xml and py files from this location and put them into ~/tools/sr_mapping/ https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping This step was not mentioned in the instruction but I thought this might be the cause. 6.I restarted the server. Once I select NGS:Mapping tool and Bwa or Bowtie I do not see the reference genome in the list. Can someone tell me what I missed or how to go about debugging it? I appreciate any kind of help ___ 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] loading file into local galaxy for first time
Hi, I just finished installed a local galaxy. I tried to load a simple small fasta file using Load Data and it is still showing as Queued (Blue). It should not take it that much to load. SO I assumed I have some issues in my installation. Can someone tell me what could ne the issue? Or how to go about debugging it? By the way, where the logs in galaxy get stores at? Appreciate your help ___ 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] loading file into local galaxy for first time
I just looked at the paster.log file while trying to load one small fasta file using Upload File or Data Library options. Here is the log I keep seeing repeating every second. 10.7.10.201 - - [01/Feb/2013:10:46:21 -0500] POST /library_common/library_item_updates HTTP/1.1 200 - http://10.7.11.190:8080/library_common/browse_library?cntrller=library_adminid=f2db41e1fa331b3ecreated_ldda_ids=2show_deleted=False; Mozilla/5.0 (Windows NT 5.2; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 Does this mean anything to you guys From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi Sent: Friday, February 01, 2013 10:02 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] loading file into local galaxy for first time Hi, I just finished installed a local galaxy. I tried to load a simple small fasta file using Load Data and it is still showing as Queued (Blue). It should not take it that much to load. SO I assumed I have some issues in my installation. Can someone tell me what could ne the issue? Or how to go about debugging it? By the way, where the logs in galaxy get stores at? Appreciate your help ___ 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 Galaxy in Windows (URGENT)
Hi Peter, Unfortunately, I am not an advanced developer in python. Although, I have 'Cygwin' in my system. Any heads up on that will be greatly appreciated? Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK From: Peter Cock p.j.a.c...@googlemail.com To: Prasun Dutta prasundutt...@yahoo.co.in Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu Sent: Friday, 1 February 2013 8:20 PM Subject: Re: [galaxy-dev] install Galaxy in Windows (URGENT) On Fri, Feb 1, 2013 at 2:33 PM, Prasun Dutta prasundutt...@yahoo.co.in wrote: Hi, I have Windows Vista and 8 in two separate laptops. I need to install a local version of Galaxy server in both the systems. I am unable to understand or follow the instructions given in your website (http://wiki.galaxyproject.org/Admin/Get%20Galaxy). Could you kindly help me or just explain me stepwise how to install it in my system? Regards, Prasun Dutta Quoting that page, The installation procedure is simple and is nearly identical for UNIX/Linux and Mac OS X. We are no longer supporting the Windows platform with our distribution, so you will have to build your own Python eggs if you want to install it on Windows (see Admin/Config/Windows for some tips). Of course, Windows users can use our public Galaxy server from their browsers. Right now you *can't* install Galaxy on Windows. Only if you were an experienced Python developer with cross-platform experience would it even be worth trying. The idea is you just run a web-browser on your (Windows) Laptop, and connect to Galaxy running on a (Linux) server. Just like you should be able to use your (Windows) Laptop to connect to the public Galaxy at http://usegalaxy.org Peter___ 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 do I allow a large group of users to RUN my workflow without them having to make a local copy
It seems strange not to be able to share workflows with groups if you can share them with individual users.. The group/role system for data libraries and the sharing system for other assets were developed concurrently. It would be reasonable (and probably not that difficult) to add groups to the sharing system. Feel free to create an issue for this, a pull request would certainly be welcome. I also have to know the exact username (email) for each user, rather than being able to choose it from a list... This is deliberate, we only expose the full user list to administrators, we would consider it a privacy issue to expose the email address of every Galaxy user to every other user. ___ 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] February 2013 Galaxy Update
Hello all, The February 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02 at http://wiki.galaxyproject.org/GalaxyUpdates/2013_02 *Highlights:* - Three new public Galaxy servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#New_Papers - New papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Who.27s_Hiring at five different institutions - GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_02#GCC2013 Training Day Topic voting, Registration, and Sponsorships - January GalaxyAdmins Web Meetuphttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#January_GalaxyAdmins_Web_Meetup slides and screencast - Other Upcoming Events and Deadlineshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Other_Upcoming_Events_and_Deadlines - Galaxy Distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Galaxy_Distributions - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Other_News If you have anything you would like to see in the March *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Thanks, Dave Clements http://wiki.galaxyproject.org/DaveClements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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 reference genome Bwa and Bowtie!
Hi Jennifer, Thank you again for your help. I am totally newbie to Galaxy so my issues could be due to my experience with it but I am getting some progress slowly though. Now, I am having totally different problem right now. I am trying to load simple file using the Galaxy GUi but it keeps telling me it is working on it but nothing really going on. I sent an email to the list but has not get anything back so far... Where can I look for galaxy logs? I am looking at the paster.log but it does not tell me much? People online keeps talking about output/log but I am not sure where to go about that. To answer your questions about SAM Tools: Following the instructions at http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I was confused at this part: Then start adding the entries for each build The file's path should include the first part of the index files' names (the base) So if they are named like reference_in.fasta.amb and are stored in /path/to/base/indices, the entry should be: reference_in /path/to/base/indices/reference_in.fasta a tab separating the two --- It talks about two columns rather than 4 columns. Also, I could not find bwa_index.loc.sample in the tool_data/ folder. Also, I had to add this entry or might be bowtie_indices.loc to too_data_table_conf.xml since it was not there by default and it was not mentioned anywhere in the instructions. For the SAM-BAM tool - in the UI, there will never be a list of genomes - that is not one of the form options. This tool either interprets the database assigned to the input dataset (option Choose the source for the reference list: Locally cashed) or allows the user to select a genome custom reference genome (option same, but History). I got lost at the point where it explains how to test it as follow: You can test your file by restarting the server and then opening SAM-to-BAM, Merge BAM files, or Generate pileup. Note that all rely on a file in the history that has a build assigned to it that is in your list of SAM Tools index builds. So you will need to set it (click the pencil icon to be able to change it) if it does not have that assigned to it already. This means that your build should be among the general builds available. - I am not really sure if I followed this. I could not see the pencil icon to change it. Can you please rephrase the above so I can follow it? Thank you... -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, February 01, 2013 9:32 AM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie! Hi Hakeem, The set up for samtools looks correct. If the problems that you had with BWA/Bowtie were due to an error in our wiki, please send in the suggested changes to me. We want this to be correct. For the SAM-BAM tool - in the UI, there will never be a list of genomes - that is not one of the form options. This tool either interprets the database assigned to the input dataset (option Choose the source for the reference list: Locally cashed) or allows the user to select a genome custom reference genome (option same, but History). So, to give this a test, run a dataset through it that has hg19 assigned as the reference and examine the results. If you are curious about custom genomes, which are used as fasta file datasets from a user's history with tools (instead of installed reference genomes), more is here: http://wiki.galaxyproject.org/Support#Custom_reference_genome Take care, Jen Galaxy team On 2/1/13 6:40 AM, Hakeem Almabrazi wrote: Thank you Jennifer for your help. I already resolved the issues with Bwa and Bowtie. I was misled with some missing instructions but I managed to resolved them by searching online. Now I am stuck at the SAM Tools displaying a reference genome :)... I will give more details at what I am doing hopefully someone can help. My reference fasta (hg10.fasta) file is located at (/usr/local/galaxy_data/hg19/samtools/) I ran the following command to build the samtools index file samtools faidx hg19.fasta This generated the hg19.fasta.fai Here is the content of the above path after running the samtools indexing command: -rwxr-xr-x 1 galaxy galaxy hg19.fasta -rw-rw-r-- 1 galaxy galaxy hg19.fasta.fai For my ~tool-data/sam_fa_indices.loc file here is the info I am using to reference the index file: IndexTABhg19TAB/usr/local/galaxy_data/hg19/samtools/hg19.fasta ### I restarted my server but I do not see anything when I go to GUI-NGS:SamTools-Sam-To-Bam-Choose the source for the reference list:HISTORY Is there something I am missing or is there anything else I need to change at this point. Regards, -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent:
Re: [galaxy-dev] install reference genome Bwa and Bowtie!
Hi Hakeem, Let me see if I can help. First, since you are running a local install, you will want to follow our distribution new briefs, posted to our wiki here, but also sent out to the mailing lists, twitter, etc. http://wiki.galaxyproject.org/DevNewsBriefs On 2/1/13 9:51 AM, Hakeem Almabrazi wrote: Hi Jennifer, Thank you again for your help. I am totally newbie to Galaxy so my issues could be due to my experience with it but I am getting some progress slowly though. Now, I am having totally different problem right now. I am trying to load simple file using the Galaxy GUi but it keeps telling me it is working on it but nothing really going on. I sent an email to the list but has not get anything back so far... This has been reported a few times, and some users have already replied that the queued jobs completed. It is most likely that the remaining jobs sent in as questions are also simply queued jobs waiting to run, but this needs to be confirmed. We will reply once that is complete. Where can I look for galaxy logs? I am looking at the paster.log but it does not tell me much? People online keeps talking about output/log but I am not sure where to go about that. What kind of other log are you looking for? As an admin of your own instance you can get really detailed and look at everything that happens, build your own queries to pull out information into files from the database, etc. For example, this is the application log table: http://wiki.galaxyproject.org/Admin/Internals/Application Logging The complete data model and other details are under here: http://wiki.galaxyproject.org/Admin/Internals To answer your questions about SAM Tools: Following the instructions at http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I was confused at this part: Then start adding the entries for each build The file's path should include the first part of the index files' names (the base) So if they are named like reference_in.fasta.amb and are stored in /path/to/base/indices, the entry should be: reference_in /path/to/base/indices/reference_in.fasta a tab separating the two --- It talks about two columns rather than 4 columns. Yes, I can see that a few of the loc file instructions are incorrect (old) where it comes to formatting. The correct instructions to follow are in the .loc files themselves. I am going to remove these sections entirely - having the content is two places makes it easy for it to get out of sync, as it is now. The definitive source for the format is the .loc file itself, whether from a repository or in the distribution. Thanks for pointing this out! Also, I could not find bwa_index.loc.sample in the tool_data/ folder. Also, I had to add this entry or might be bowtie_indices.loc to too_data_table_conf.xml since it was not there by default and it was not mentioned anywhere in the instructions. BWA was moved to the tool shed and out of the Galaxy distribution some months ago. Do you mean that the BWA repository in the Tool Shed did not have instructions it it for how to set up the installation with respect to data? This is currently true, and is something that is under current discussion/work (how to correctly and fully document each repository so that all dependencies are self-included - not only for repos generated by the Galaxy team but everyone!). The feedback that this is important is on target with what we thought was needed - we appreciate that you took the time to let us know. For the SAM-BAM tool - in the UI, there will never be a list of genomes - that is not one of the form options. This tool either interprets the database assigned to the input dataset (option Choose the source for the reference list: Locally cashed) or allows the user to select a genome custom reference genome (option same, but History). I got lost at the point where it explains how to test it as follow: You can test your file by restarting the server and then opening SAM-to-BAM, Merge BAM files, or Generate pileup. Note that all rely on a file in the history that has a build assigned to it that is in your list of SAM Tools index builds. So you will need to set it (click the pencil icon to be able to change it) if it does not have that assigned to it already. This means that your build should be among the general builds available. - I am not really sure if I followed this. I could not see the pencil icon to change it. The pencil icon is in the dataset box. This wiki explains, but just look at any dataset in your history and you will find it in the upper right corner: http://wiki.galaxyproject.org/Learn/Managing%20Datasets#Dataset_Icons_.26_Text Click on the pencil icon to reach a set of tabs that permit the editing of a dataset's attributes, including the assigned reference genome. For your test and the tool you mentioned, you will want
[galaxy-dev] Can't specify workflow parameters for integer values
Hello,
I created a simple workflow with an input file and the 'Select first'
tool. I wanted the value to be a parameter ${value}. I am able to save the
workflow and see the little grey parameters box at the top of the workflow
editor.
When I try to run this workflow I get a yellow box at the top of the
window stating the following:
Problems were encountered when loading this workflow, likely due to tool
version changes. Missing parameter values have been replaced with default.
Please review the parameter values below.
I do not however see an error in paster.log
When I reopen the workflow in the editor I get a popup window saying
'Workflow loaded with changes'
Problems were encountered loading this workflow (possibly a result of tool
upgrades). Please review the following parameters and then save.
Step 2: Select first
Value no longer valid for 'Select first', replaced with default
I am running two instances of Galaxy (Jan. 11 distributuion) and this
occurs in both of my instances. Will other workflows as well. But it
appears to only occur for integer parameters...not text parameters.
Any help would be much appreciated.
Liisa
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Re: [galaxy-dev] File Upload doesn't generate any activity
On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold sgroenew...@idtdna.com wrote: We’ve installed a local instance of Galaxy and are having trouble with the first step of uploading files. The only thing that will currently upload is text pasted into the URL/Text box. Any attempt to upload a file using the Browse File box not only fails, it never even starts. It’s as if the Execute button is disabled. I’ve tried changing the ajax-upload parameter to “false” in tools/data_source/upload.xml (as mentioned in a workaround posted to the list by Daniel Blankenburg in Aug 2012). I’ve also tried using different browsers (including Internet Explorer) and going the route of Adding Data Libraries as Admin. None of those attempts have worked. Am I missing a configuration setup? Could there be permissions issues on the Galaxy machine? This sounds like the same issue I've reported to this list, which Carl and others have been kind enough to look at. I think their look is still in progress but hopefully there will be some news about it soon. Here is that thread: http://dev.list.galaxyproject.org/error-uploading-file-with-fresh-installation-this-request-returned-None-from-get-history-td4657958.html#a4657960 Dan Thanks. Steve ___ 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] install Galaxy in Windows (URGENT)
On Feb 1, 2013, at 11:12 AM, Peter Cock wrote: On Fri, Feb 1, 2013 at 3:48 PM, Prasun Dutta prasundutt...@yahoo.co.in wrote: Hi Peter, Unfortunately, I am not an advanced developer in python. Although, I have 'Cygwin' in my system. Any heads up on that will be greatly appreciated? Cygwin is a useful system for running Unix/Linux tools under Windows, and according to this old email from Nate you would need to use it: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003671.html More recently a couple of people tried this and ran into problems: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007132.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007180.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007182.html For the simplest install and maintenance, choose what the Galaxy team use: Linux Even if you can get the framework to run, many tools with C dependencies are going to be a nightmare to use since the dependencies will almost certainly not compile. The easiest solution these days if you really have no access to a Linux system (the cloud is a good choice here) is probably to install Linux in a VM on your Windows system. This can be done for free with a VM platform like VirtualBox. --nate Regards, Peter ___ 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 use the API when using a proxy server
I'm glad that worked, Thon. Let us know if you run into any other problems with the API in a proxy set up. Carl On Thu, Jan 31, 2013 at 7:58 PM, Anthonius deBoer thondeb...@me.com wrote: Hi Carl, I am using the submit and get functions from the scripts/api/common.py I actually found that I just need to add authentication to the calls, so I added this code def authenticate(url, u, p): auth_handler = urllib2.HTTPBasicAuthHandler() auth_handler.add_password(realm='GALAXY@GHI. Please log in with your Windows account', uri=url, user=u, passwd=p) opener = urllib2.build_opener(auth_handler) # ...and install it globally so it can be used with urlopen. urllib2.install_opener(opener) def make_url( api_key, url, args=None ): # Adds the API Key to the URL if it's not already there. if args is None: args = [] argsep = '' if '?' not in url: argsep = '?' if '?key=' not in url and 'key=' not in url: args.insert( 0, ( 'key', api_key ) ) return url + argsep + ''.join( [ '='.join( t ) for t in args ] ) def get( api_key, url, user, pw ): # Do the actual GET. url = make_url( api_key, url ) authenticate(url, user, pw) try: return simplejson.loads( urllib2.urlopen( url ).read() ) except simplejson.decoder.JSONDecodeError, e: print URL did not return JSON data sys.exit(1) . . . /code This will authenticate for each call and it seems to work nicely (if you add the authenticate step to each of the functions, like I did here for get Thon On Jan 31, 2013, at 11:44 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Hello Anthonius, Can you elaborate on how you're invoking the API? How are you calling it? Thanks, Carl On Wed, Jan 30, 2013 at 6:30 PM, Anthonius deBoer thondeb...@me.comwrote: Hi, I am trying to use the API with my galaxy server running behind a proxy server. How do I pass username/password information to the API so it can actually run? If I use the regular API calls I get a access denied... 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] History not updating automatically
Joachim, is your history panel still not updating or did you find a
solution from the info in this thread?
If not, can you post the contents of the alert/popup message?
Thanks,
Carl
On Tue, Jan 29, 2013 at 5:26 AM, Joachim Jacob |VIB|
joachim.ja...@vib.bewrote:
Hi,
I have a similar - but not identical issue. The history panel is not being
updated: I have to restart Galaxy to see the updated panel.
It appears only to happen after an error relating to the history API of
Galaxy (it's a popup error, and I have closed it).
My apache config (thanks for any hints and tweaks to improve my setup).
[galaxy@galaxy conf.d]$ cat galaxy_web.conf
NameVirtualHost 157.193.230.103:80
VirtualHost 157.193.230.103:80
ServerName galaxy.bits.vib.be
Proxy balancer://galaxy
BalancerMember http://localhost:8080
BalancerMember http://localhost:8081
BalancerMember http://localhost:8082
BalancerMember http://localhost:8083
BalancerMember http://localhost:8084
BalancerMember http://localhost:8085
BalancerMember http://localhost:8086
BalancerMember http://localhost:8087
BalancerMember http://localhost:8088
BalancerMember http://localhost:8089
BalancerMember http://localhost:8090
BalancerMember http://localhost:8091
BalancerMember http://localhost:8092
/Proxy
RewriteEngine on
RewriteLog /tmp/apacheGalaxy.log
### LDAP authentication will be implemented later
# Location /
# AuthType Basic
# AuthBasicProvider ldap
# AuthLDAPURL
ldap://smeagol.vib.be:389/DC=**vib,DC=local?sAMAccountNamehttp://smeagol.vib.be:389/DC=vib,DC=local?sAMAccountName
# AuthLDAPBindDN vib\administrator
# AuthLDAPBindPassword tofillin
# AuthzLDAPAuthoritative off
# Require valid-user
# # Set the REMOTE_USER header to the contents of the LDAP query
response's uid attribute
# RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}
# /Location
RewriteRule ^/static/style/(.*)
/home/galaxy/galaxy-dist/**static/june_2007_style/blue/$1
[L]
RewriteRule ^/static/scripts/(.*)
/home/galaxy/galaxy-dist/**static/scripts/packed/$1
[L]
RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/**static/$1 [L]
RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/**static/favicon.ico
[L]
RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/**static/robots.txt [L]
RewriteRule ^(.*) balancer://galaxy$1 [P]
/VirtualHost
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 01/28/2013 09:02 PM, Langhorst, Brad wrote:
Nate:
I used the config from the wiki directly…
Location /
…
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}**e
...
/Location
but I also had a section like this below it...
# Location /api
# Satisfy Any
# Allow from all
# /Location
I thought that the /api location would inherit the auth and headers stuff
of it's container, but that's not true.
Commenting the api location fixes the problem form e.
Brad
On Jan 28, 2013, at 2:35 PM, Nate Coraor n...@bx.psu.edu
wrote:
Hi Brad and Sajoscha,
Is there any chance that your proxy configurations are not passing the
username in the REMOTE_USER header when the request is to an /api path?
Could you provide the relevant portions of your proxy server configs?
Thanks,
--nate
On Jan 28, 2013, at 7:12 AM, Langhorst, Brad wrote:
Hi Sajoscha:
I have exactly the same problem… it started about a month ago.
Also with external ldap auth.
I have not yet investigated in detail, since it's not crippling - just
annoying.
Brad
On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de
wrote:
Hi list,
I have a weird problem after updating to the latest version.
After doing the update as usual, the history panel is not updating
automatically anymore. And when I press refresh, I get an javascript popup
saying:
Error getting history updates from the server.
Forbidden
Also, in the log I see the following:
galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as
'(null)' externally, but has a cookie as 'sa...@embl.de' invalidating
session
We are using LDAP to connect to Galaxy, but I don't know if this has
something to do with the problem. As I said, it was working perfectly fine
before the update.
Does someone know the problem or has any ideas?
Thanks for your help,
Sajoscha
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--
Brad Langhorst
langho...@neb.com
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Re: [galaxy-dev] File Upload doesn't generate any activity
We've also seen that same error in our startup log: == Traceback (most recent call last): File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py, line 447, in _load_plugin module = __import__( module_name ) File /Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py, line 232 worker = threading.Thread( ( name=LwrJobRunner.thread-%d % i ), target=self.run_next ) ^ SyntaxError: invalid syntax === And we are also having trouble uploading files. Originally, even attempts to add files via the Admin Data Libraries process wouldn't work. That seems to have been resolved (coincidentally? or causally?) after another user completed a general upload via a URL. But even now, uploading a specific file with the Get Data - Upload File process is still non-responsive. Either the Execute button never does anything at all, or the upload process appears in History and turns blue but never completes. -Original Message- From: Dan Tenenbaum [mailto:dtene...@fhcrc.org] Sent: Friday, February 01, 2013 3:14 PM To: Stephen Groenewold Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] File Upload doesn't generate any activity On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold sgroenew...@idtdna.com wrote: We've installed a local instance of Galaxy and are having trouble with the first step of uploading files. The only thing that will currently upload is text pasted into the URL/Text box. Any attempt to upload a file using the Browse File box not only fails, it never even starts. It's as if the Execute button is disabled. I've tried changing the ajax-upload parameter to false in tools/data_source/upload.xml (as mentioned in a workaround posted to the list by Daniel Blankenburg in Aug 2012). I've also tried using different browsers (including Internet Explorer) and going the route of Adding Data Libraries as Admin. None of those attempts have worked. Am I missing a configuration setup? Could there be permissions issues on the Galaxy machine? This sounds like the same issue I've reported to this list, which Carl and others have been kind enough to look at. I think their look is still in progress but hopefully there will be some news about it soon. Here is that thread: http://dev.list.galaxyproject.org/error-uploading-file-with-fresh-installation-this-request-returned-None-from-get-history-td4657958.html#a4657960 Dan Thanks. Steve ___ 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] Can't specify workflow parameters for integer values
Hi Liisa,
Thank you for reporting this bug. A fix has been committed
(https://bitbucket.org/galaxy/galaxy-central/commits/73bb36c4ee3b34c3ca32ed830b4f91df79b971c5)
and will be available in an upcoming release. Please let us know if you
encounter additional issues.
Thanks for using Galaxy,
Dan
On Feb 1, 2013, at 2:59 PM, Liisa Koski wrote:
Hello,
I created a simple workflow with an input file and the 'Select first' tool. I
wanted the value to be a parameter ${value}. I am able to save the workflow
and see the little grey parameters box at the top of the workflow editor.
When I try to run this workflow I get a yellow box at the top of the window
stating the following:
Problems were encountered when loading this workflow, likely due to tool
version changes. Missing parameter values have been replaced with default.
Please review the parameter values below.
I do not however see an error in paster.log
When I reopen the workflow in the editor I get a popup window saying
'Workflow loaded with changes'
Problems were encountered loading this workflow (possibly a result of tool
upgrades). Please review the following parameters and then save.
Step 2: Select first
Value no longer valid for 'Select first', replaced with default
I am running two instances of Galaxy (Jan. 11 distributuion) and this occurs
in both of my instances. Will other workflows as well. But it appears to only
occur for integer parameters...not text parameters.
Any help would be much appreciated.
Liisa
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[galaxy-dev] installing phylop
I am trying to setup PhyloP in galaxy. In the add_scores.loc file it says we need the phyloP46way.primate.bw (BigWig) file. #hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw Is there a downloadable bigwig files somewhere for hg19 that I can use? From the instructions on bigwig, it looks like we have to create a bigwig file from the wig files. Thanks, -Dina ___ 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] installing phylop
Hi Dina, These data are available from USCS in their downloads area at http://genome.ucsc.edu. See the left side bar for the 'Downloads' link, then navigate to the genome release and track files (are clearly labeled). Best, Jen Galaxy team Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org On Feb 1, 2013, at 9:45 PM, Dinanath Sulakhe sula...@mcs.anl.gov wrote: I am trying to setup PhyloP in galaxy. In the add_scores.loc file it says we need the phyloP46way.primate.bw (BigWig) file. #hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw Is there a downloadable bigwig files somewhere for hg19 that I can use? From the instructions on bigwig, it looks like we have to create a bigwig file from the wig files. Thanks, -Dina ___ 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] installing phylop
Hi Jen, Thanks for your reply. I looked at these phyloP46way-Primates datasets here : http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/primates/ They don't seem to be in bigwig format and also there is one file per chromosome. The PhyloP's add_scores.loc instructions give an impression that it may take just one bigwig file. If this is the right data, do i need to convert them into bigwig format and how? And how to configure add_scores.loc to provide multiple files (per chromosome)? Thanks, -Dina On Feb 1, 2013, at 11:55 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Dina, These data are available from USCS in their downloads area at http://genome.ucsc.edu. See the left side bar for the 'Downloads' link, then navigate to the genome release and track files (are clearly labeled). Best, Jen Galaxy team Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org On Feb 1, 2013, at 9:45 PM, Dinanath Sulakhe sula...@mcs.anl.gov wrote: I am trying to setup PhyloP in galaxy. In the add_scores.loc file it says we need the phyloP46way.primate.bw (BigWig) file. #hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw Is there a downloadable bigwig files somewhere for hg19 that I can use? From the instructions on bigwig, it looks like we have to create a bigwig file from the wig files. Thanks, -Dina ___ 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/
