Re: [galaxy-dev] Lost in tool dependencies

Hi Lionel! > Hi Björn, > > > There is a version in the testtoolshed, I can migrate it if you like and > > if you can confirm that you can install it :) > > I'd be very interested in the infernal wrapper! I'll try to install it. Hope you like it! > > The problem is that you do not have defined

[galaxy-dev] Tool's toolshed page does not get updated after uploading new version

Hi all, My issue: I have put a new version of a tool in our local toolshed (via 'hg push'). Now, going to the tool's page, still the old version of the README is displayed. When browsing the repository, the new (last uploaded) version is there. In addition, the tool's page show the latest rev

Re: [galaxy-dev] Solved Tool's toolshed page does not get updated after uploading new version

Hmm, now the tool's page is updated. Problem solved. Perhaps a browser cache issue or something alike. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/06/2013 10:22 AM, Joachim Jacob | VIB | wrote: Hi all, My issue: I have put a new version of a tool in ou

[galaxy-dev] API question: is it possible to start exporting histories

Hi all, Is it currently possible to export histories via the API? I have one user who want to download and store her data. Total sizes of all her histories combined is about ~700GB. I think this is a typical API job: to list all her histories, start 'exporting to file' all of them, and final

Re: [galaxy-dev] Lost in tool dependencies

Hi Björn, Moving the dependencies to tool_dependencies.xml worked as a charm. Thanks for your help! I tested the infernal package, and it worked as well! However, the package_infernal_1_1rc4, owned by the iuc, is enough for my purpose and already on the main tool shed, so no need to push the

Re: [galaxy-dev] Lost in tool dependencies

Hi, > Moving the dependencies to tool_dependencies.xml worked as a charm. > Thanks for your help! Great! > I tested the infernal package, and it worked as well! However, the > package_infernal_1_1rc4, owned by the iuc, is enough for my purpose and > already on the main tool shed, so no need t

[galaxy-dev] options from_dataset evaluation in workflow

Dear all, in one of my tools I'm populating a list of possible choices from a file in the history using the tag. Now using the tool as part of a workflow, the choices are not calculated at the setup stage, but I have to enter free-text and Galaxy seems to evaluate whether that's a legal choice onl

Re: [galaxy-dev] API question: is it possible to start exporting histories

> Is it currently possible to export histories via the API? Not possible yet but is definitely something we'd like to implement and/or see from a community contribution. Best, J. ___ Please keep all replies on the list by using "reply all"

[galaxy-dev] workflow_execute.py failing!

Hi, I have been trying to use workflow_execute.pl to execute a workflow that has ~50 steps. I keep getting this error after running for few seconds knowing I could run the same workflow from the GUI without any issue. HTTP Error 500: Internal Server Error 500 Internal Server Er

Re: [galaxy-dev] Display BAM and bigWig on UCSC when require_login = False

Dear all, We experienced the same issue. In the current state, either we can't display the data using a genome browser, either we have to grant anonymous access. Was it considered a concern that datasets may be accessed without a login? If so, may I suggest to add an option so that we permit the d

[galaxy-dev] Looking for brave testers. New barcode splitter outputing splitted datasets directly to the history.

Hi, I was wondering if I could get someone to test this new barcode splitter I wrote. The main reason for me to duplicate the already great fastx-toolkit based splitter, is so I can use galaxy's multiple output capabilities. You can find this tool in the testtoolshed for now(after some more testi