[galaxy-dev] organizing histories in galaxy

Hi, Is there a way to organize related histories together into a "project" or folder? I realize in a lot of cases, a pipeline is designed for processing of a single sample, while a study typically consists of multiple samples that go through the same processing. They are then put together fo

Re: [galaxy-dev] possible to undelete a history?

Hello Edward, Have the user go into their account, use "Options -> Saved Histories" and click on "Advanced Search" at the top of the page. The refreshed page will have a link to view deleted histories "deleted: ". They can then check these and use the "undelete" button at the bottom of the pa

[galaxy-dev] possible to undelete a history?

An unfortunate user emailed me and said he accidentally deleted his histories. :(( How can I help him recover these? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and ot

Re: [galaxy-dev] Apache Configuration for Exporting Histories and Workflows

Hi John, John Chilton wrote, On 07/22/2011 11:40 AM: > We have Galaxy behind an apache proxy, and apache is taking care of > the authentication. If I want to enable exporting workflows and > histories to other galaxy instances do I just need to disable the > authentication checks for locations "/h

Re: [galaxy-dev] Upload of images - jpg/png - "binary file contains inappropriate content"

Based on the error message you gave, I assume the following code in ~/lib/galaxy/datatypes/sniff.py is presenting the problem. if check_binary( filename ): if ext not in unsniffable_binary_formats and not datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ):

Re: [galaxy-dev] Newer Version of Cufflinks Wrapper

I just hit reply. Would be easier if when I hit reply it automatically sent the email back to the list. That's how other mailing lists that.I'm on work. Thanks for the hg info. Thanks, Ilya Sent from my iPhone On Jul 22, 2011, at 6:32 AM, "Jeremy Goecks" mailto:jeremy.goe...@emory.edu>> wrot

Re: [galaxy-dev] Metadata in Galaxy Tool Shed

Hello Lance, It looks like the repository metadata was successfully generated. Normally this should take no more than a few seconds, but the server hosting our tool shed sometimes gets bogged down with other cpu intensive processes, so on some occasions, things don't work as expected. We're w

Re: [galaxy-dev] new data type.

Hi, Hans, Thanks for the link. I figured out the problem. It turned out the data type nexus was registered twice in the datatypes_conf.xml and the second one was not using the right type. THanks, Luobin On Fri, Jul 22, 2011 at 1:19 AM, Hans-Rudolf Hotz wrote: > Hi Luobin > > It is difficult t

Re: [galaxy-dev] Upload of images - jpg/png - "binary file contains inappropriate content"

Hi Greg, I used that link when trying to create the support. The jpg datatype was already present in the datatypes_conf.xml ( ) , so I first made it available at upload -> display_in_upload=True. As far as I understood, if galaxy doesn't have to guess what the format is, this would be sufficien

[galaxy-dev] Metadata in Galaxy Tool Shed

I recently created a new repository in the galaxy tool shed for the cutadapt tool and "imported" my old hg repository into it. However, it doesn't seem to be picking up the metadata correctly. Does this take time, or is there something I need to do to get the metadata generated correctly? Al

[galaxy-dev] Apache Configuration for Exporting Histories and Workflows

Hello All, We have Galaxy behind an apache proxy, and apache is taking care of the authentication. If I want to enable exporting workflows and histories to other galaxy instances do I just need to disable the authentication checks for locations "/history/export_archive" and "/workflow/for

[galaxy-dev] Scroll bars not present using i.e.

http://test.g2.bx.psu.edu/ Cheers, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern icho...@illumina.com 858-202-4582 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage y

Re: [galaxy-dev] error reading tool from path (epigraph.xml, epigraph_test.xml, access_libraries.xml)

This is due to a bug that was corrected in change set 5819:0f15591f2acd, which should be available in our main Galaxy instance, as well as the distribution, within the next few weeks. If you need it sooner, you can pull it from our development repo. Sorry for the inconvenience. Greg Von Kuste

Re: [galaxy-dev] Where to find the toolconfig parser code?

On 07/22/2011 04:53 PM, Peter Cock wrote: On Fri, Jul 22, 2011 at 3:50 PM, Samuel Lampa wrote: The #if#else syntax, in for example this tool example: ... is that something that you galaxy parses itself (tried to grep for some matching-code, but found nothing so far), or are that some python

[galaxy-dev] error reading tool from path (epigraph.xml, epigraph_test.xml, access_libraries.xml)

Dear all, I installed a local galaxy using the latest codebase yesterday. During the startup, the loading of 3 tool wrappers are failed: epigraph.xml, epigraph_test.xml, access_libraries.xml. Similar errors were reported in http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01839.html Ha

Re: [galaxy-dev] Where to find the toolconfig parser code?

On Fri, Jul 22, 2011 at 3:50 PM, Samuel Lampa wrote: > One follow up question then: > > The #if#else syntax, in for example this tool example: > >  ... > > ... is that something that you galaxy parses itself (tried to grep for some > matching-code, but found nothing so far), or are that some pytho

Re: [galaxy-dev] Where to find the toolconfig parser code?

One follow up question then: The #if#else syntax, in for example this tool example: ... sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} #if $source.index_source == "history": --ref_file=$source.ref_file #else --ref_file="Non

Re: [galaxy-dev] Where to find the toolconfig parser code?

Ah, thanks! I somehow missed that file altogether ... // Samuel On 07/22/2011 03:59 PM, Greg Von Kuster wrote: Samuel, Look at the parse(0 method in the Tool class in ~/lib/galaxy/tools/__init__.py for most of it. You should be able to find everything you need from there. Greg Von Kuster

Re: [galaxy-dev] Error moving tool-data dir ... bowite indexes missing

Ross, I think I don't understand what you mean. Do you mean the actual reference to the files contained in the loc file? I have all non-relative paths to the bowtie indexes (snippet below). The last column is an additional column for some plotting tools to have a sensible short name and works f

Re: [galaxy-dev] Where to find the toolconfig parser code?

Samuel, Look at the parse(0 method in the Tool class in ~/lib/galaxy/tools/__init__.py for most of it. You should be able to find everything you need from there. Greg Von Kuster On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote: > Quick question to you devs, > > I need to find the code where t

[galaxy-dev] Where to find the toolconfig parser code?

Quick question to you devs, I need to find the code where the tool configs are parsed ... especially the "free-text" if-else clauses in the command-tag. Could someone point me to the file? TIA // Samuel -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University,

Re: [galaxy-dev] Newer Version of Cufflinks Wrapper

Ilya, A patch is fine for a one-time fix; this is easy with Mercurial: % hg diff > my_patch.patch However, if you plan to contribute to Galaxy on a regular basis, we encourage you to fork Galaxy and maintain your own Bitbucket repository. Finally, please send all emails to our mailing lists

Re: [galaxy-dev] Upload of images - jpg/png - "binary file contains inappropriate content"

Hello Jelle, There are a few things you need to do to add support for a new data type. The steps are described here: http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes Greg Von Kuster On Jul 22, 2011, at 8:49 AM, Jelle Scholtalbers wrote: > Hi all, > > I would like to be able to u

[galaxy-dev] Error moving tool-data dir ... bowite indexes missing

On our up-to-date galaxy_central version I have successfully moved the database/files directory to mounted storage. After adapting the universe_wsgi.ini it works fine after galaxy restart. Now the tool-data dir becomes bigger and bigger and I wanted to move that to mounted storage as well. I mo

[galaxy-dev] Upload of images - jpg/png - "binary file contains inappropriate content"

Hi all, I would like to be able to upload images to my Galaxy instance - in particular jpg/png to data libraries. I can't however find out how to overcome the problem of inappropriate content in binary file. How to go about? When I create a sniffer class in the galaxy.datatypes.images.py that alw

Re: [galaxy-dev] new data type.

Hi Luobin It is difficult to guess without seeing your code. So, assuming you followed the steps described in the wiki (http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes), I guess you just made a typo somewhere (since this has happen to me several times when adding a new datatype).