[galaxy-dev] visulaization of tree produced by raxml

Hi, Do you guys have any suggestions on what tool I should use to construct tree from the output produces by raxml. There are some tree builder in Galaxy that seem not to be working with this output (correct me if I am wrong). The developer of raxml recommend dendroscope which is not available in

[galaxy-dev] June 2, 2014 Galaxy Distribution

June 2, 2014 Galaxy Distribution *News Brief **Highlights:* * Dataset Collections introduced * Changes to database build (dbkey) organization * Enhancements to Tool c

Re: [galaxy-dev] Unable to access admin after install EMBOSS 5 from galaxy test repo

Hello Cristian, I've just instaled the emboss_5 repository along with all dependencies from the test Tool Shed, so I'm not sure what configuration in your Galaxy environment may be causing the behavior you're seeing. Currently the only way to uninstall a repository is via the Galaxy admin UI.

Re: [galaxy-dev] Uploading files to galaxy from a folder

Iyad, Yes, that's a different topology. We run on a shared cluster, so the Galaxy head nodes (app + db) sit next to the cluster, and the galaxy user has no special powers outside the head node, though the filesystem is completely cross-mounted. Regards, Curtis -Original Message-

Re: [galaxy-dev] Uploading files to galaxy from a folder

Hi Curtis, I recall coming across the external chown script you mentioned but for some reason it wasn't working as expected, which is why I opted to insert in my own function in upload.py. I think the documentation in the universe_wsgi.ini didn't match up with how the script worked, so I didn'

Re: [galaxy-dev] Uploading files to galaxy from a folder

John, For us, it's not just a question of deleting the file, but of having permission to do python's copystat (see stack trace below). We've tried a variety of permission combinations, including sticky group permissions, various setfacl's and moving the directory on or off the same filesystem

Re: [galaxy-dev] tool dependencies fail

Galaxy is not sourcing env.sh I tried sourcing it before restarting galaxy and it worked. So that's the issue. How do I get galaxy to source env.sh? $ ls -lh tool_dependencies/hhsuite/ total 8 drwxr-xr-x@ 11 iphan SBRI\Domain Users 374B Jun 2 10:54 2.0.16/ lrwxr-xr-x 1 iphan SBRI\Domain U

Re: [galaxy-dev] tool dependencies fail

Hello Dave, I got interrupted before I could reply to the second suggestion from Jorrit: > Not sure about specifying the absolute path for the tool dependency dir, >but I always use it. using the absolute path of the tool dependency dir had no effect. > Also, my env.sh neither has a #!/bin/bash

Re: [galaxy-dev] tool dependencies fail

Isabelle, In order to help track down the cause of this issue, could you provide the output of the following two commands? ls -lh tool_dependencies/hhsuite/ ls -lh tool_dependencies/hhsuite/default/ --Dave B. On Mon 02 Jun 2014 01:29:44 PM EDT, Isabelle Phan wrote: I tried hhsuite and

Re: [galaxy-dev] tool dependencies fail

I tried hhsuite and that had no effect. I. -- Message: 3 Date: Sat, 31 May 2014 03:51:55 +0200 From: Bj?rn Gr?ning To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool dependencies fail Message-ID: <538935bb.7020...@gmail.com> Content-Type: text/plain

Re: [galaxy-dev] New tool on TestToolShed still not tested

Peter, Thank you for reporting this issue, which should be resolved in 13703:8caa7f4d72c7. Tonight's test run should correctly install and test blast_rbh. --Dave B. On Tue 27 May 2014 10:23:15 AM EDT, Peter Cock wrote: Thanks - I'll leave this until next week then. Peter On Tue, May 27,

Re: [galaxy-dev] Cluster Admins - Call for experiences/issues encountered

Hi, Yes, I am aware of such. I had intended to update the Cluster docs as it's the more appropriate page, perhaps linking to it from the community log page. I was hoping that people might send in their experiences so I could aggregate them and write the entries for them. There's always a lot of

Re: [galaxy-dev] Cluster Admins - Call for experiences/issues encountered

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Bjoern, Yes, I am aware of such. I had intended to update the Cluster docs as it's the more appropriate page, perhaps linking to it from the community log page. I was hoping that people might send in their experiences so I could aggregate them an

Re: [galaxy-dev] stdout in history

Hi All, I think it makes a lot of sense to allow disabling the addition of stderr and/or stdout to dataset.info on a per tool/output dataset basis. I’ve added a Trello card for this here: https://trello.com/c/hC5HABnr. Not sure when anyone might have a chance to look into it, but pull requests

Re: [galaxy-dev] Cluster Admins - Call for experiences/issues encountered

Hi Eric, thanks for caring about that issue. Do you know about Galaxy Community Hubs? https://wiki.galaxyproject.org/Community/ The community is encouraged to share experience under that page. Maybe you can add yours to that page as well? Cheers, Bjoern Am 27.05.2014 18:32, schrieb Eric Ra

[galaxy-dev] Installing galaxy with Apache

Hi, this thread is likely related to this one: http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td4654499.html 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/Apa