Re: [galaxy-dev] Workflow Queue

2012-09-13 Thread Hans-Rudolf Hotz
Hi Edward Select 'view' instead of 'run' in your workflow list. This will give you a nice (human readable) overview of all the steps, or select the download option to get an xml describing your workflow. Regards, Hans On 09/13/2012 03:20 AM, Edward Hills wrote: Hi Galaxy team, I am

Re: [galaxy-dev] Size of the genome indexes repos in Galaxy Main

2012-09-13 Thread Nate Coraor
On Sep 12, 2012, at 8:28 PM, Derrick Lin wrote: Hi guys, Just a quick question about the total size of the genome indexes just made available via rsync server? Hi Derrick, The full size is around 3 TB. --nate Cheers, Derrick

[galaxy-dev] FTP problem

2012-09-13 Thread Rémy Dernat
Hi, I follow this tutorial to configure FTP with galaxy : wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP However, even if I can [ log into / upload file to / donwload file to ] my ftp server with my Galaxy account, I can not retrieve these data on my Galaxy Web server. It says : Your FTP

Re: [galaxy-dev] environment variables and paths for toolshed tools

2012-09-13 Thread Greg Von Kuster
Hello David, I've just committed change set 7656:6aadac8026cb to the Galaxy central repository that provides the ability to do what you need here. It would be great if you could try things out and let me know if you run into any problems. I've been working with nikhil-joshi's

Re: [galaxy-dev] problem in Fastq tool

2012-09-13 Thread Daniel Blankenberg
Hi Felix, Thanks for reporting this error, it has been fixed in revision 7663:cc064ff4249b. Please let us know if you encounter additional issues. Thanks for using Galaxy, Dan On Sep 10, 2012, at 12:23 PM, Felix Homa wrote: Hello, We noticed a problem with the tool Filter Fastq. It

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-13 Thread Lance Parsons
Actually, I think that is exactly the issue. I DO have 3:f7a5b54a8d4f installed. I've run into a related issue before, but didn't fully understand it. I believe what happened was: 1) I pushed revision 3:f7a5b54a8d4f to the tool shed which contained the first revision of version 0.2 of the

Re: [galaxy-dev] tool_data_table.xml and *.loc not installed with repository

2012-09-13 Thread Greg Von Kuster
Hello Birgit, I've committed a fix for this issue in change set revision 7668:802413bc137b, which is currently running on the test tool shed and is currently available only in the Galaxy central repository. This fix will be include in the ext Galaxy distribution scheduled for the end of next

Re: [galaxy-dev] toolshed upload problem

2012-09-13 Thread Greg Von Kuster
Hi David, I committed a fix for this issue in changeset 7662:c4ced3262d0d, which is currently available only in the Galaxy central repository. The fix will be available in the next Galaxy release scheduled for the end of next week. Thanks for reporting this problem, and sorry for the

Re: [galaxy-dev] enable emboss tools

2012-09-13 Thread Greg Von Kuster
Hi Paul, It seems that you probably did not use the Emboss tools in your local Galaxy instance before (maybe you have a new instance). If this is the case, you can install the emboss_datatypes repository and the emboss_5 repository from the main Galaxy tool shed using the Admin UI features on

Re: [galaxy-dev] Size of the genome indexes repos in Galaxy Main

2012-09-13 Thread Derrick Lin
Thanks Nate, D On Thu, Sep 13, 2012 at 10:43 PM, Nate Coraor n...@bx.psu.edu wrote: On Sep 12, 2012, at 8:28 PM, Derrick Lin wrote: Hi guys, Just a quick question about the total size of the genome indexes just made available via rsync server? Hi Derrick, The full size is around 3

Re: [galaxy-dev] Small enhancment to the tarball parsing.

2012-09-13 Thread Greg Von Kuster
Hello Bjorn, I've committed your patch in change set revision 7669:5088185a5bca, which is currently running on the test Galaxy tools shed. The fix will be moved to the main Galaxy tool shed at the time of the next Galaxy release, currently scheduled for the end of next week. Regarding the

Re: [galaxy-dev] enable emboss tools

2012-09-13 Thread Greg Von Kuster
Hi Paul, You have to be running the latest Galaxy dist release from https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance. Your repository tip should be e6444e7a1685. Greg Von Kuster On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote: Hmm, ok this tool shed is all new to me.

Re: [galaxy-dev] enable emboss tools

2012-09-13 Thread Paul Tanger
Thanks for your help with this. So I updated to the latest version, but didn't read the instructions about creating a tools directory and so I have repositories stuck in limbo, like described here:

[galaxy-dev] markupsafe module confliction problem

2012-09-13 Thread Fenglou Mao
Galaxy imported a library which already existed in the python system folder. See the error message below. Is that because RedHat 6 used a python-marksafe, but Galaxy installation program did not recognize it? Or Galaxy require a higher version of markupsafe module? /home/x/work/galaxy-dist/

Re: [galaxy-dev] enable emboss tools

2012-09-13 Thread Greg Von Kuster
Hi Paul, You should be able to get things working using the same sql command in the email below. This process will be a new UI feature in the next Galaxy release. Greg Von Kuster On Sep 13, 2012, at 6:15 PM, Paul Tanger wrote: Thanks for your help with this. So I updated to the latest

Re: [galaxy-dev] enable emboss tools

2012-09-13 Thread Paul Tanger
Ok I just gave up and did a fresh install and it seems to work. Thanks for your help. On Thu, Sep 13, 2012 at 7:17 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Paul, You should be able to get things working using the same sql command in the email below. This process will be a new UI

[galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

2012-09-13 Thread Derrick Lin
hi guys, I have been trying to clean up some old histories and datasets on our local galaxy. I have spotted one very old dataset file with big size didn't get removed no matter what. I went to check the reports webapp, that dataset isn't on the largest unpurged data files list (despite it has

[galaxy-dev] reinstall

2012-09-13 Thread Paul Tanger
So I successfully added the emboss tools to galaxy, but I failed to create a tool panel section for them. So I thought I would uninstall them and install them again, this time creating a tool panel section. I'm following the instructions here (

Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

2012-09-13 Thread Jeremy Goecks
Cleaning up the datasets manually is the best suggestion for now. We're planning to enhance the clean up scripts to automatically delete history export files soon. Best, J. On Sep 13, 2012, at 10:37 PM, Derrick Lin wrote: hi guys, I have been trying to clean up some old histories

Re: [galaxy-dev] [galaxy-user] No output produced.....

2012-09-13 Thread Jeremy Goecks
The problem is likely your use of the from_work_dir attribute. I can see by the logging code that you're using an old(er) version of Galaxy, and it's likely that this attribute isn't functioning correctly in your instance. We've recently improved the implementation of from_work_dir, and

Re: [galaxy-dev] Orphan dataset created by history Export to File (possibly a bug?)

2012-09-13 Thread Derrick Lin
Thanks Jeremy, I am sure it's trivial for us to do a manual clean up Cheers, D On Fri, Sep 14, 2012 at 1:05 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Cleaning up the datasets manually is the best suggestion for now. We're planning to enhance the clean up scripts to automatically delete