[galaxy-dev] August 2014 Galaxy Newsletter

Hello all, The August 2014 Galaxy Update Newsletter is out. Here's a preview of what's inside: - GCC2015 will be held in Norwich, United Kingdom, 6-8 July 2015

Re: [galaxy-dev] new_file_path questions

On Fri, Aug 1, 2014 at 4:16 AM, Geert Vandeweyer wrote: > Hi, > > I'm running into issues with our galaxy installation regarding the > new_file_path setting: > > 1/ clean up : > > Can I safely delete all contents in the tmp folder using a cronjob, or > manually when galaxy is (not) runnin

Re: [galaxy-dev] TestToolShed failure, Exception: History in error state.

On Thu, Jul 31, 2014 at 12:29 PM, Peter Cock wrote: > On Thu, Jul 31, 2014 at 5:21 PM, bjoern.gruen...@googlemail.com > wrote: >> Hi Peter, >> >> >> 2014-07-31 10:57 GMT+02:00 Peter Cock : >> >>> Hi Dave, >>> >>> You are right that on closer inspection I've mixed tool_dependencies.xml >>> and rep

[galaxy-dev] bx version conflict causes failure for some tools (e.g. subtract interval tool)

see: https://biostar.usegalaxy.org/p/8095/ I can work around the problem by adding a stdio block to these tools, how should the underlying problem be solved? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist ___

[galaxy-dev] Error while installing tools from main toolshed: "HTTPerror : HTTP error 307 : temporary redirect"

Hi, I'm trying to install tools from the main toolshed, but I keep getting the same error regardless of the tool that I'm installing HTTPError: HTTP Error 307: Temporary Redirect URL: http://localhost:8080/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repos

Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

That was it! Yay! I'll add a Trello card to have this info gem added to the docs. Thanks, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___

Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

Hmmm... you know what. I tested this out and it looks like Galaxy expects the git repo to be named the same as the package name in your tool dependencies file ffp-phylogeny. If you change the git command to: git clone https://github.com/apetkau/ffp-3.19-custom.git *ffp-phylogeny* I think it sho

Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

A little more info: ls -a # ls -a STDOUT . .. # # ls -a STDERR so I guess the .git archive is being unpackaged somewhere else! After lunch I'll return to ex

Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

Sadly, ./configure --disable-gui --prefix=$INSTALL_DIR yeilds install error: /bin/sh: ./configure: No such file or directory But file must be there since previous git step is carried out ok: ... # git reset --hard 1819482db93bf0025c2588b526

Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

Hey Damion, You should be able to do *./*configure --disable-gui ... to get it to work (that is, make sure the full path to the configure command is given). At least I think that's probably what's going on. Aaron On Fri, Aug 1, 2014 at 12:32 PM, Dooley, Damion wrote: > Hi folks, > > Having a

[galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

Hi folks, Having a difficult time with coding the "configure" step in this new tool_dependency.xml file, namely that an error "/bin/sh: configure: command not found" results when I try to install my beta development tool from a local test toolshed (which is downloading and installing other tool

Re: [galaxy-dev] galaxy install nginx

The order is not very important… however I would install nginx and postgres at the same time, then galaxy. brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 1, 2014, at 10:10 AM, ngsf...@hygenomics.com wrote: dear sir:

[galaxy-dev] Announcement: Galaxy IPython Integration - interactive programming in Galaxy

Hi all, we proudly present the first release of the Galaxy IPython project. Galaxy IPython is a visualization plugin which should enable Galaxy users with coding skills to easily process their data in the most flexible way. With this plugin, it is possible to analyse and post-process data wit

[galaxy-dev] galaxy install nginx

dear sir: nginx postgress galaxy which one first install ? ngsf...@hygenomics.com ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy l

Re: [galaxy-dev] Packaging tools with language specific dependencies

Hi BJörn, We have run into some problems with the perl environment. This might also affect other tools that rely on a shebang with absolute paths to the interpreter. Details below. During the installation of the perl package (we tried package_perl_5_18 from main and testing toolshed), the cpanm s

[galaxy-dev] new_file_path questions

Hi, I'm running into issues with our galaxy installation regarding the new_file_path setting: 1/ clean up : Can I safely delete all contents in the tmp folder using a cronjob, or manually when galaxy is (not) running. I have gathered almost 700Gb and >72K files on data there apparen