Re: [galaxy-dev] I can't see or access pictures in FastQC

2012-06-07 Thread Dorset, Daniel C
Hi Ross, thanks for the reply! I ran FastQC from the command line, and it did give the proper output. Furthermore, FastQC generating the proper output when I run it from Galaxy. However, Galaxy is having trouble accessing the files. If I go into the filesystem, I can find all of the files in

Re: [galaxy-dev] LookupError: No section 'main' (prefixed by 'server') found in config

2012-06-07 Thread Rémy Dernat
Hi Nate, I try it with a script for galaxy service, but it did not work. I successfully did it with one daemon file for each process... regards. 2011/8/26 Nate Coraor n...@bx.psu.edu Hi Iry, By default, PasteScript is looking for a section named [server:main]. With this config, you can

Re: [galaxy-dev] TopHat fusion

2012-06-07 Thread Jeremy Goecks
There's a Tophat2 wrapper in galaxy-central right now that you're welcome to try, but it's still under development and may be buggy and is still subject to (potentially) major changes. I'd guess that Tophat2 support will make it to beta near the end of this month and be available on the public

Re: [galaxy-dev] Incomplete datasets when dowloaded from history

2012-06-07 Thread Jennifer Jackson
Hello Jean-François, For larger files, or if complete downloads seem to be a problem, using curl at a command or Terminal prompt is a great option. The syntax is: % curl -O 'copied-link-from-dataset-disc-icon'

[galaxy-dev] Sharing data in Cistrome

2012-06-07 Thread Päivi Pihlajamaa
Hi, I am trying to share my files/history in Galaxy/Cistrome with my colleague, but the 'Share with user' link gives the following error. Could you please help me, am i doing something wrong or is there a bug in the system? Best regards, Päivi Server Error URL:

[galaxy-dev] Group by c1: max[c2] --skipped 11489 invalid lines starting with line 3. Value '' in column 0 is not numeric

2012-06-07 Thread Michael Thang
input file example in galaxy:WASH7P 0.305384KLHL17 6.4404GLTPD1 22.8633PUSL122.9327CPSF3L 0.446421SAMD11 0.0267019 output:AAAS then the error message complaint is on the tile column.After updating R to latest version the grouping function is no longer working. I have been

Re: [galaxy-dev] Incomplete datasets when dowloaded from history

2012-06-07 Thread Jean-Francois Payotte
Hi Jennifer, Thank you for your answer. Although using curl command might be a good solution to overcome the incomplete downloads issue, this solution might not be enough user-oriented (as I don't think our users are familiar with using the command line). Anyway, we have developed a tool

Re: [galaxy-dev] Sharing data in Cistrome

2012-06-07 Thread Alban Lermine
Hi, Did you have special characters (é, à,...) in the email of the person you try to share with? If so, try whitout this special characters (è - e or à - a), it should works.. Bests, Alban Le 07/06/2012 16:26, Päivi Pihlajamaa a écrit : Hi, I am trying to share my files/history in

Re: [galaxy-dev] Load Balancer config doesn't work

2012-06-07 Thread Nate Coraor
On Jun 1, 2012, at 4:36 AM, julie dubois wrote: Hi, After several post in an Apache Forum, I've solve any problem of my apache configuration to enable load balancer configuration. It seems work but when I launch my galaxy application, I arrive in this web page : Service temporarily

[galaxy-dev] How to upload local files in Galaxy

2012-06-07 Thread Mehmet Belgin
Hi Everyone, I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is

Re: [galaxy-dev] How to upload local files in Galaxy

2012-06-07 Thread Langhorst, Brad
Mehmet: It's not important how the files get there, they could be moved via ftp, scp, cp, smb - whatever. Galaxy will use that directory to import from no matter how the files arrive. I found that confusing at first too. Brad On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote: Hi Everyone, I am

Re: [galaxy-dev] How to upload local files in Galaxy

2012-06-07 Thread Mehmet Belgin
Brad, Thank you for your fast reply! Looks like library_import_dir is for admins and there is another library option for users. I will try with that one and see if the files appear in the GUI. Thanks! = Mehmet Belgin, Ph.D.

Re: [galaxy-dev] AttributeError: 'module' object has no attribute 'FakeSocket'

2012-06-07 Thread Nate Coraor
On May 22, 2012, at 11:18 AM, Peter Cock wrote: On Tue, May 22, 2012 at 4:14 PM, Sarah Diehl di...@immunbio.mpg.de wrote: Thanks Peter! It's very likely that I have the exact same problem, because I also have CentOS and needed to compile Python. In that case make sure you've done this:

Re: [galaxy-dev] I can't see or access pictures in FastQC

2012-06-07 Thread Ross
Hi, Daniel, Sorry to say I'm unable to explain this problem with your local instance - it works fine on all of mine and on main. What do you see when you type hg tip in the root of your Galaxy clone? The current tip is hg tip changeset: 7243:37352829fedd If this is an up to date clone and you

Re: [galaxy-dev] I can't see or access pictures in FastQC

2012-06-07 Thread Dorset, Daniel C
I appreciate you taking the time to help! I'm almost positive it's a local configuration issue, like you said, but without knowing how Galaxy generates or parses its internal links (in the form of [Galaxy web address]/datasets/[16 character hash]/display/[filename] ) it's tough to know how to

Re: [galaxy-dev] I can't see or access pictures in FastQC

2012-06-07 Thread Ross
Hi, Daniel, The configuration suggested at http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy is what you followed to set your proxy up? That obfuscated link hash element is generated from internal database ids to help secure against malicious users viewing specific datasets - not something

[galaxy-dev] Galaxy Test Not Producing Output

2012-06-07 Thread Kipper Fletez-Brant
Hi List, I'm trying to write a test for Galaxy and it fails on the result of the test differing from the expected output. As the output of diff (below) lists nothing but local_file data, I'm assuming that the issue is that no output is being generated by the test. The test config is a series

Re: [galaxy-dev] populating history with input files automatically from remote site?

2012-06-07 Thread John Chilton
Hello Nik, I have put together a project that builds heavily on mi-deployment that does some of what you want to do (and probably a bunch of things you don't), but you could hopefully pull out just the parts you need. The idea behind the project is to build really cheap cloud galaxy instances by

[galaxy-dev] Tool Shed Workflow

2012-06-07 Thread John Chilton
I have read through the documentation a couple times, but I still have a few questions about the recent tool shed enhancements. At MSI we have a testing environment and a production environment and I want to make sure the tool versions and configurations don't get out of sync, I would also like