[galaxy-dev] Main Galaxy Tool Shed is running the next-stable branch

Hello all, The main Galaxy Tool Shed is now running the next-stable branch ( e6813f244a2a (next-stable) tip ) in preparation for next upcoming Galaxy release. Please let us know if you encounter anything strange or broken and we'll get things fixed asap. The main Tool Shed will be updated to

Re: [galaxy-dev] package_r_2_11_0 and ggplot2

Am 29.07.2014 um 22:45 schrieb Evan Bollig: Hey Bjoern, I'm trying to use variant_recalibrator, xy_plot and other tools that depend on package_r_2_11_0 and require ggplot2 to be installed. Since CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a better idea to update the package

Re: [galaxy-dev] How can I populate a data_collection output ?

Hi John, Is there any documentation that explains how dataset collections work? I'd like to learn more about it. Thanks, David On Tue, Jul 29, 2014 at 3:20 PM, John Chilton wrote: > Hello Julie, > > Right now Galaxy can implicitly create collections by running a tool > that takes in a singl

Re: [galaxy-dev] package_r_2_11_0 and ggplot2

Hey Bjoern, I'm trying to use variant_recalibrator, xy_plot and other tools that depend on package_r_2_11_0 and require ggplot2 to be installed. Since CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a better idea to update the packages the depend on those versions to R 3.0 or 3.1?

Re: [galaxy-dev] How can I populate a data_collection output ?

Hello Julie, Right now Galaxy can implicitly create collections by running a tool that takes in a single input or a paired dataset over say a list of inputs or a list of paired inputs but tools cannot explicitly create dataset collections. I think Galaxy's current capabilities add a lot of usefu

Re: [galaxy-dev] package_r_2_11_0 and ggplot2

Hi Evan, do you have somehow access to this tarball? Than we can put it on https://github.com/bgruening/download_store I use that to host R packages to save them for reproducibility. Can I install another package_r and have packages that depend on package_r_2_11_0 use the newer version? I d

[galaxy-dev] package_r_2_11_0 and ggplot2

I want to install ggplot2 into package_r. The library ggplot2 is no longer available from the CRAN mirror for R v2.11.0. How do you guys handle this situation? Can I install another package_r and have packages that depend on package_r_2_11_0 use the newer version? -Evan Bollig Research Associate

Re: [galaxy-dev] Error while installing DESeq-hts

Hey Greet and Bjoern, Sorry for the troubles with dependencies during the automated installation procedure! I will add tool dependency file, when I get some time during this weekend :) Vipin | Rätsch Lab On Tue, Jul 29, 2014 at 10:06 AM, Björn Grüning wrote: > Hi Geert and Vipin, > > I might

Re: [galaxy-dev] IE 11 issues

That's what I was getting as well. It looks like this is an issue with IE11's event management API and our version of jQuery. I'll see if I can find a fix or alternately see if an updated jQuery will still cause this error. If this is blocking your analyses, I'd unfortunately recommend using eith

Re: [galaxy-dev] galaxy won't start

Thanks for the fast reply! I tried it in the clean environment and it works. I somehow totally missed that step when setting this up! So do I need to add these 2 steps to my startup script? /usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env . ./galaxy_env/bin/activate Thanks, Dor

Re: [galaxy-dev] Error while installing DESeq-hts

Hi Geert and Vipin, I might also consider the DESeq package and the wrappers from galaxytools if you plan to update your wrappers. https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_deseq2_1_2_10 @Geert: impressive documentation! Thanks a lot for sharing! Bj

Re: [galaxy-dev] galaxy won't start

Hi Dori, If you haven’t updated galaxy or manipulated the eggs at all, then it might be an updated system python module interfering with galaxy’s resolution of the pyyaml we ship. Can you try running galaxy from an clean virtualenv? (https://wiki.galaxyproject.org/Admin/Config/Performance/Prod

Re: [galaxy-dev] Error while installing DESeq-hts

I know this is a very old entry to the mailing list, but I thought this might be useful for some people. Recently, I set up DESeq-hts and its siblings on our galaxy instance. To succeed, I performed the steps below. @vipin: would you consider revising the tool_dependencies.xml for these tool

[galaxy-dev] galaxy won't start

I'm suddenly getting this error today when I tried to restart Galaxy: Starting galaxy... Some eggs are out of date, attempting to fetch... Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg One of Ga