galaxy-dev June 2014

galaxy-dev@lists.galaxyproject.org

64 participants
110 discussions

Re: [galaxy-dev] to put or not to put a tool suite into the
by Kandalaft, Iyad 06 Jun '14

06 Jun '14

Hello Wolfang, I agree that developing the Galaxy "way" is not always "easy". The main advantage of galaxy's toolshed is a point that you stated in your introduction "reproducibility". Galaxy's toolshed enforces proper versioning of tool wrappers and its dependency on underlying software. Hence, reproducibility is taken care of automatically between galaxy and the toolshed. In addition, it automates one of the steps for your users: "dependencies on samtools, etc, etc". Some of these dependencies are already packages in the galaxy central toolshed (such as samtools). Therefore, using the tool shed is advantageous. Pushing the repositories to the central tool shed is a way of giving back to the galaxy/research community that you and I depend on. Regards, Iyad Kandalaft Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: Iyad.Kandalaft(a)agr.gc.ca Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada

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Installing galaxy with Apache
by Matthias Enders 06 Jun '14

06 Jun '14

Hi, this thread is likely related to this one: http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td4654499.… I installed Galaxy on a Ubuntu Server 12.04 system. I followed the instruction on the link mentioned above and this one: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy Now my issue is: When I got this configuration in my /etc/apache2/sites-available/default : RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] Galaxy is visible at www.my_server_url.de<http://www.my_server_url.de> but not at www.my_server_url.de/galaxy<http://www.my_server_url.de/galaxy> Following the later URL I got this message: Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET /galaxy<http://www.gsa.npz.de/galaxy>. Reason: DNS lookup failure for: localhost:8080http: ________________________________ Apache/2.2.22 (Ubuntu) Server at www.my_server_url.de Port 80 When I change the configuration like this: (make the second line a comment): RewriteEngine on #RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] Galaxy is visible both at www.my_server_url.de<http://www.my_server_url.de> and at www.my_server_url.de/galaxy<http://www.my_server_url.de/galaxy> When I completely remove this part, the "It works!" standard page of apache is displayed. The configuration in my universe.ini is as follows: host = 127.0.0.1 [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy Can you please help me with this issue? I want to see the "It works!" page at www.my_server_url.de<http://www.my_server_url.de> and galaxy only at www.my_server_urla.de/galaxy. Thanks in advance! Kind regards Matthias Enders

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galaxy is not sourcing tool environment
by Isabelle Phan 05 Jun '14

05 Jun '14

I am using env.sh to manage my tool dependencies: # tool_dependency_dir/hhsuite/2.0.16/env.sh export HHPRED_DIR=/opt/galaxy-dist/tool_dependencies/hhsuite/default export HHLIB=${HHPRED_DIR}/lib/hh export PATH=${HHPRED_DIR}/bin:${HHLIB}/scripts:$PATH Galaxy is not sourcing it. I have to manually source it before I restart Galaxy. I am following "Using the env.sh file" and cannot get it to work. What am I missing? Any help greatly appreciated, thanks, Isabelle

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Manual Tool and dependency installation
by Ravi Alla 05 Jun '14

05 Jun '14

Hi All, Due to the nature of our cluster we are not allowed to have compilers on our webserver, which is where our galaxy instance runs. Because of this tool dependencies and tools that need to be compiled fail to install through the galaxy tool shed webpage. Is there a way for me to install dependencies and tools manually? For example I am trying to install the GATK2 wrapper. This depends on samtools-0.1.19 from iuc which in turn requires ncurses-5.9. Is there instructions somewhere as to where to install these tools such that they are tied to the GATK2 wrapper? Pardon me if this is a naive question, but I am really out of sorts here. Thank you Ravi

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Re: [galaxy-dev] tool dependencies fail
by Isabelle Phan 05 Jun '14

05 Jun '14

I tried <requirements> <requirement type="package">hhsuite</requirement> </requirements> and that had no effect. I. ------------------------------ Message: 3 Date: Sat, 31 May 2014 03:51:55 +0200 From: Bj?rn Gr?ning <bjoern.gruening(a)gmail.com> To: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] tool dependencies fail Message-ID: <538935BB.7020905(a)gmail.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi, can you try: <requirements> <requirement type="package">hhsuite</requirement> </requirements> Hope that helps, sorry for the short answer I'm too tired :) Bjoern

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About GALAXY customisation
by Patrick Tran Van 05 Jun '14

05 Jun '14

Hi, I've done a local installation of Galaxy. Everything work but I just have some questions about customisation: 1)How can I modify the main page (for example: new image, twitter integration etc.) as seen on the main page of galaxy (https://usegalaxy.org/) ? 2)How can I write title on the toolbox menu (eg : NGS Toolbox Beta) 3)Is it possible to upload a file without copy it and without being as admin but as simple user ? I know we can upload a file without copy in Galaxy (https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?ac…) but I want to do it without being admin. Thanks for your help Patrick Tran Van INSA Lyon 4ème année Bio-Informatique et Modélisation

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Pre pull-request: CLI and hidden data
by Ganote, Carrie L 05 Jun '14

05 Jun '14

Hi Devs, I'd like to open up some discussion about incorporating some code bits into the Galaxy distribution. My code is here: https://bitbucket.org/cganote/osg-blast-galaxy First off, I'd like to say that these changes were made initially as hacks to get Galaxy working with a grid interface for our nefarious purposes. For us, the results have been spiffy, in that we can offload a bunch of Blast work off of our own clusters and onto the grid, which processes them fast on a distributed set of computers. In order to do this, I wanted to be able to take as much control over the process as I could. The destination uses Condor, but it used condor_dag to submit jobs - that means I would have to modify the condor job runner. The destination needed to have the files shipped over to it first - so I had to be able to stage. This made lwr attractive, but then I would need to guarantee that the server at the other end was running lwr, and since I don't have control of that server, this seemed less likely to be a good option. The easiest thing for me to understand was the cli runner. I could do ssh, I could do scp, so this seemed the best place to start. So I started by trying to figure out which files needed to be sent to the server, and then implementing a way to send them. I start with stdout, stderr and exit code files. I also want to stage any datasets that are in the param_dict, and anything that is in extra_files_path. Then we alter the command line that is run such that all the paths make sense on the remote server, and to make sure that the right things are run remotely vs. locally (i.e., metadata.sh is run locally after job is done). Right now, this is done by splitting the command line on a specific string, which is not robust for future changes to the command_factory, but I'm open to suggestions. So, here's one hack. The hidden data tool parameter is something I hijacked - as far as I can tell, hidden data is only used for Cufflinks, so it seemed safe. I use it to send the shell script that will be run on the server (but NOT sent to the worker nodes). It needed to be a DATA type so that my stager would pick it up and send it over. I wanted it to be hidden because it was only used by the tool and it should not need to be an HDA. I made changes to allow the value of the hidden data to be set in the tool - this would become the false_path of the data, which would then become its actual path. Please have a look, and ask questions, and if there are improvements needed before anything is considered for pulling, let me know. I'd like to present this at the Galaxy conference without having vegetables thrown at me. Thanks! -Carrie Ganote National Center for Genome Analysis Support Indiana University

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2014 Galaxy Community Conference June 6 Registration Deadline (this Friday)
by Dave Clements 04 Jun '14

04 Jun '14

Hello all, Regular registration for the 2014 Galaxy Community Conference (GCC2014, https://wiki.galaxyproject.org/Events/GCC2014) closes this Friday, June 6. After that late registration is still open, but registration rates *go up 100%.* GCC2014 is all about high-throughput biology. It's in Baltimore, from June 30 through July 2. The full program is posted, and includes - Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> - 15 sessions on 12 topics in 5 parallel tracks with topics ranging from *Visualizing NGS data *to* Galaxy installation and administration* - 26 talks <https://wiki.galaxyproject.org/Events/GCC2014/Program#Day_1:_Main_Meeting.2…> including a keynote by Steven Salzberg, and 25 other talks by researchers and industry leaders - 25 Posters <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Poster_Abstracts> - and counting - we still have space for a few more <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Abstract_Submission> - Lightning Talks - Present your rsesarch in two fast paced sessions. - Birds-of-a-Feather <https://wiki.galaxyproject.org/Events/GCC2014/BoFs> - Gather with other researchers with common interests and challenges (and propose one <https://wiki.galaxyproject.org/Events/GCC2014/BoFs#Want_to_plan_a_BoF.3F> for your own area of interest) - The first ever GCC Hackathon <https://wiki.galaxyproject.org/Events/GCC2014/Hackathon> (only 8 spaces left) Please do let us know if you have any questions. We would love to see you in Baltimore. Thanks, Dave Clements > *2014 Galaxy Community Conference (GCC2014) > <http://galaxyproject.org/GCC2014>* http://galaxyproject.org/GCC2014 > June 30 - July 2, 2014 > Homewood Campus > <http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…> > > Johns Hopkins University > <http://jhu.edu/> Baltimore, Maryland > <http://visitors.baltimorecity.gov/>, United States -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Galaxy customized tool config file
by Vipin TS 04 Jun '14

04 Jun '14

Hello dev-team, With the current state, is it possible to write an interactive page for a tool in Galaxy? In my case, I m considering to build a tool page with JavaScript embed in XML file, my expectation is to behave the Galaxy tool page as google translate page with option instant translation on (display the same text content in the next box). I have checked the Admin/Tools/ToolConfigSyntax, not sure whether I missed anything related this. any comments ? thanks, Vipin galaxy.cbio.mskcc.org

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Re: [galaxy-dev] Move galaxy/database (SQLite) to a new location
by Kandalaft, Iyad 04 Jun '14

04 Jun '14

Neil, >From what I understand, galaxy uses sqlalchemy for all its databse operations regardless of the database engine that is actually hosting the data. I suspect that galaxy uses a default sqlalchemy connection string by default even when you don't specify one, which points to databases/universe.sqlite. I also suspect that you can modify the location of the database by doing the following in universe_wsgi.ini database_connection = sqlite:////absolute/path/to/foo.db Let us know if that works. Regards, Bioinformatics Application Developer Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: Iyad.Kandalaft(a)agr.gc.ca Telephone | Téléphone 613- 759-1228 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada From: <Neil.Burdett(a)csiro.au> To: <galaxy-dev(a)lists.bx.psu.edu> Subject: [galaxy-dev] Move galaxy/database (SQLite) to a new location Message-ID: <25BF49C282C04548A60517FFB251C20D2F737E67(a)exmbx03-cdc.nexus.csiro.au> Content-Type: text/plain; charset="iso-8859-1" Hi, we have the default setup for galaxy hence using SQLite database and all data store in the same location as the galaxy install. In Universe_wsgi.ini file there is an entry # Dataset files are stored in this directory. #file_path = database/files How do we go about moving the database to a new location? We don't really want to delete the data already present in the database just move it to a new location. If we modify file_path and restart wouldn't that cause further problems as some data would be in one location and other in another location. Is it even possible to move the database once it has been created and has data in it? Thanks Neil

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galaxy-dev June 2014