- galaxy-dev - lists.galaxyproject.org

Recently Used Histories
by Jonathan Strickland 11 Jun '13

11 Jun '13

Hello all! I've recently started using Galaxy, and it's a fantastic piece of software. However, I had a question about a possible feature, and any suggestions on how to implement it. My use case involves working with a lot of histories, and I need to jump back and forth between them fairly frequently. However, it's a bit inconvenient to have to click on the "Options" button on the rightmost pane, "Saved Histories" in the drop-down menu, and select my history on the main pane. An easier way to switch between histories that were recently used could definitely benefit me, and perhaps other people too. I propose an easily accessible list with links to the 5 most recently visited histories. I took a look at the source, but as I'm unfamiliar with Django and the Galaxy codebase, I thought it might be best to come here for advice. My initial thought was to show the last 5 most recently updated histories underneath the "History Lists" in the options menu. However, that would probably cause trouble when working when Shared Histories that other people are working on, jumping up to the top of the list whenever anyone edits them. The best solution I could think of was to have some sort of list of the histories visited. When the user selects a history, that history is pushed to the top of the stack, and if there are more than 5 items in the stack, the least recent history is popped off. Ideally, the user wouldn't need to go back to the "Saved Histories" or "Histories Shared With Me" grid when working with a few different histories at once. I'm also not sure where the user's state is stored, so I don't know where I would put this variable. I'm also not sure if there's any hooks or anything when selecting a history that I could take advantage of to push it to the top of the user's stack. An issue with this approach is that an item from a history may be open on the main pane, and the user can select another history without going to either grid of histories. This problem doesn't currently occur, because the only way to select a different history is by opening up the history list on the main screen. The main pane needs to be changed to something else upon changing histories, but I don't have any ideas as to what would be best. Perhaps the default "Analyze Data" screen? Sorry for so many questions! Any answers or suggestions would be much appreciated :) I'm also curious if anyone would benefit from this feature besides myself!

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problems with exporting or importing data
by Edlund, Anna 11 Jun '13

11 Jun '13

Hi. I have uploaded fasta files on the main galaxy server through my FileZilla program. In want to transfer them to the Galaxy at the Huttenhower Lab (see http://huttenhower.org/galaxy/root) page and to do that go to history list when I am logged in at both locations and I select 'Import a History from an archive'. I paste the url address from the main galaxy server (where my archive is located) and select submit. Then I waited for 2 days and nothing was transferred? I am clearly doing something wrong and would really like you input asap. Thank you very much!! Best regards, Anna Edlund My user name is aedlund(a)jcvi.org<mailto:aedlund@jcvi.org>

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minor SQLAlchemy PostgreSQL issue
by Richard Burhans 11 Jun '13

11 Jun '13

The SQLAlchemy "postgres" dialect was renamed to "postgresql". Changing: database_connection = postgres:///... to: database_connection = postgresql:/// in the ini file causes Galaxy (tool_shed in my case) to fail to start as the "postgres" dialect is mentioned by name a few places in the code. Not a big deal, but I figured I'd report it. -rico

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Failed runtime validation of To
by Sameer Dixit 11 Jun '13

11 Jun '13

Hey all, I've been trying to run a workflow on Galaxy, which basically attempts to establish a correlation between the Chip-Chip, Polymerase binding and Dnase Hypersensitivity data. The input would be these 3 files, I am initially performing a liftover on the Chip-Chip data to convert from hg18 to hg19 and then using the output to establish the correlation. The following error keeps coming up 'Failed runtime validation of To (An invalid option was selected, please verify)' Can anyone please tell me what this might mean? This came up while attempting to run the following tool Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/lib/galaxy/jobs/runners/__init__.py", line 121, in prepare_job job_wrapper.prepare() File "/galaxy/home/g2main/galaxy_main/lib/galaxy/jobs/__init__.py", line 656, in prepare self.tool.handle_unvalidated_param_values( incoming, self.app ) File "/galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py", line 2343, in handle_unvalidated_param_values self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) File "/galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py", line 2382, in handle_unvalidated_param_values_helper raise LateValidationError( message ) LateValidationError Any assistance would be highly appreciated!! Thanks -Sameer

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Re: [galaxy-dev] Installing Galaxy EC2
by Daniel Gorelik 11 Jun '13

11 Jun '13

Hello, Thanks all, but it it turns out my problem was that the line saying to use the 0.0.0.0 host was commented out.. That was stupid.. Thank you, Daniel On Jun 11, 2013, at 6:46 AM, Quang Trinh <quang.trinh(a)gmail.com> wrote: > Hi Dan and Joachim > You can also try what my students put together, which is based on a config file and more simple. > > https://github.com/modENCODE-DCC/Galaxy/blob/master/docs/README.how.to.laun… > > Thanks, > > Q > > > > > > On Tue, Jun 11, 2013 at 3:30 AM, Joachim Jacob | VIB | <joachim.jacob(a)vib.be> wrote: > Hi Daniel, > > Make also sure you use correct firewall settings ('security groups') in EC2. They are described the Galaxy wiki (http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted?highlight=%28secu…) but there are some small differences with the setting applied by CloudLaunch (http://dev.list.galaxyproject.org/Cloudman-missing-security-rules-in-wiki-p…) > > Set by CloudLaunch (during my latest launch): > Ports Protocol Source CloudMan > 1-65535 tcp sg-61ba790a > *1-65535 udp sg-61ba790a * > *-1 icmp sg-61ba790a * > 20-21 tcp 0.0.0.0/0 <http://0.0.0.0/0> > 22 tcp 0.0.0.0/0 <http://0.0.0.0/0> > 80 tcp 0.0.0.0/0 <http://0.0.0.0/0> > 30000-30100 tcp 0.0.0.0/0 <http://0.0.0.0/0> > 42284 tcp 0.0.0.0/0 <http://0.0.0.0/0> > > > Cheers, > Joachim > > Joachim Jacob > Contact details: http://www.bits.vib.be/index.php/about/80-team > > > On 06/10/2013 10:54 PM, Daniel Blankenberg wrote: > Hi Daniel, > > This should work fine. You'll need to make sure that you have the host setting in your universe_wsgi.ini like: > > host = 0.0.0.0 > > and that the port 8080 is open/accessible in the security group settings for the instance in AWS. > > > Thanks for using Galaxy, > > Dan > > On Jun 10, 2013, at 4:42 PM, Daniel Gorelik wrote: > > Hello all, > > I have a question: does anyone know if it is possible to install Galaxy on an EC2 instance as you would on a local machine, not using CloudMan, and then view it in the web browser by going to public_ip:8080? I have been trying and it has not been working for me. > > > Thanks so much! > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >

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Toolshed tool doesn't exist error after installation from toolshed
by Simon Gladman 11 Jun '13

11 Jun '13

Hi all, Looked for this in the list but couldn't find it. Admittedly I was using gmail to search the list so I may have missed it - apologies if so. I have put a very simple tool into a local toolshed (latest version of toolshed) which just consists of an xml wrapper and a perl script in the repository. (attached) I want to test it prior to putting it in the main toolshed.. When I install the tool into my galaxy (latest-stable version) it installs ok. I then go to run the tool and it loads the interface quite happily but upon execute it says tool doesn't exist. I think its looking in the wrong folder on the server for the tool. In the main galaxy window: Tool ' galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0' does not exist, kwd={'tool_state': u'80025569356339643261396332633035356535356161303366316533393935313439613834366130616239363a3762323235663566373036313637363535663566323233613230333032633230323236343631373436313733363537343232336132303232333233323232376471002e', 'runtool_btn': u'Execute', 'refresh': u'refresh', 'dataset': u'22'} In the server log: galaxy.webapps.galaxy.controllers.tool_runner ERROR 2013-06-11 14:23:14,434 index called with tool id ' galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0' but no such tool exists 128.250.103.244 - - [11/Jun/2013:14:23:14 +1100] "POST /tool_runner/index HTTP/1.1" 200 - " https://galaxy-vbc-test.monash.edu/tool_runner?tool_id=galaxy-dev.genome.ed…" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/27.0.1453.110 Safari/537.36" The tool is installed in (via the toolshed install process): shed_tools/ galaxy-dev.genome.edu.au/repos/slugger/fasta_stats/94469f4c8a55/fasta_stats Any ideas? Cheers, Simon Gladman

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Galaxy job will stay in waiting under DRMAA runner until manually trigger a command line submission
by Linda Cham 11 Jun '13

11 Jun '13

Hi. Running standalone Galaxy stable_2013.06.03 version on RH6.2 with postgresl db with GPFS filesystem. Setup via the directions in http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster to run all jobs through the LSF DRMAA runner. job_conf.xml: -------------------- <job_conf> <plugins> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="lsf"> <destination id="lsf" runner="drmaa"/> </destinations> </job_conf> Scheduler and Galaxy were started. Submit a FASTQ groomer job on a FASTQ file under Galaxy. The groomer job in History will stay in GREY "Job is waiting to run" state until one physically go onto the node and submits a command line job through the scheduler. Once that command line job (e.g. sleep 5) is submitted then the groomer job will show up in the scheduler's job queue and galaxy's HISTORY will now show it as running. I can submit another groomer job after this and it will show up as running. At times, one will see this type of scenario again where one has to manually start a job under the scheduler on the command line to trigger the galaxy's jobs to start running under the scheduler. Is there some setup I am missing in the job_conf.xml above or a flag not set in universe_wsgi.ini? Searching the Galaxy web, I had read that one can set the track_jobs_in_database=True to trigger it to look in memory or database. But that didn't work either. Wonder if anyone seen this type of issue with any runners and have any suggestions on how to debug and fix this. Thanks. Linda

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Failing test in tool shed not shown
by Björn Grüning 11 Jun '13

11 Jun '13

Hi, my augustus repository is shown under the summary page "Latest revision: failing tool tests" but I could not see any failing test in the repository. http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus Cheers, Björn

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Installing Galaxy EC2
by Daniel Gorelik 11 Jun '13

11 Jun '13

Hello all, I have a question: does anyone know if it is possible to install Galaxy on an EC2 instance as you would on a local machine, not using CloudMan, and then view it in the web browser by going to public_ip:8080? I have been trying and it has not been working for me. Thanks so much!

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How to Install Bowtie?
by Nicholas Kline 10 Jun '13

10 Jun '13

Hi, Our lab recently installed a local version of Galaxy on Mac OS X 10.8 and can access it at localhost:8080. Now we are trying to install Bowtie version 1 but need help getting it to work. At this point we do not see the tool listed on the left side of the Galaxy menu. Here are the exact steps we followed: 1. create directory /Users/administrator/galaxy-dist/tools_dependencies 2. in universe_wsgi.ini set tool_dependency_dir = tools_dependencies 3. in /etc/paths append /Users/administrator/galaxy-dist/tools_dependencies 4. create tools_dependencies/bowtie/1.0.0/bin 5. create symbolic link tools_dependencies/bowtie/default to directory in step 4 6. download Bowtie, extract it, and copy binaries to tools_dependencies/bowtie/1.0.0/bin Problem: Bowtie is still not appearing in menu on the left side of Galaxy Thanks!

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