Hi all,
Is anyone working on (or has already created) wrappers for GATK 3.0?
Specifically, I'm looking for a wrapper for genotypeGVCFs, but it seems
like I would want all the GATK wrappers to be updated. Any help is highly
appreciated!
- Nik.
--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC
Thanks John. I guess I'm looking at options "enable_tool_shed_install"
and "tool_shed_install_config_file" that were added in rev 6398 and
dropped in rev 6747 when the tool migration scripts were added. I
don't know why they were dropped, but they would be immensely useful
today.
This is related t
Hey Evan,
Out of curiosity, are you trying to update MSI's CLIA pipeline to
utilize tool shed installed tools? (It sounds kind of like yes.)
I don't think that file you mentioned exists in either place - is it a
typo or maybe a configuration file with overridden location in
universe_wsgi.ini?
Re
Hello dev-team,
With the current state, is it possible to write an interactive page for a
tool in Galaxy?
In my case, I m considering to build a tool page with JavaScript embed in
XML file, my expectation is to behave the Galaxy tool page as google
translate page with option instant translation o
I want to setup a tool_shed_install.xml to roll out tools at first
boot for Galaxy.
1) Is it possible to get Galaxy to generate this based on the tools
currently installed from the tool shed?
2) Is it required to list every tool provided by each repository, or
can I simply add the repository to t
Hello Evan,
Thanks a bunch for the error report! I can confirm the problem and a
hack to avoid it can be found here -
https://github.com/jmchilton/galaxy-central/commit/306a86558a7ee7be1bc2d68cd939b16b5f1863d4.patch.
I am going to give someone more familiar with the core GUI stuff a
chance to fix
Hmm... I am not exactly sure the best way to display this data but I
wanted to mention that it is all available via the API (thanks to Kyle
Ellrott). I believe full provenance information (parameters, stdout,
stderr, tool_id, etc...) is available even for permanently deleted
datasets.
I just added
Hi,
I am currently working on some user-service functionalities on a local
version of galaxy (cistrome actually) and I am looking for a way to save
some job details outside of Galaxy.
This would allow the users to consult those even after the datasets are
deleted from Galaxy (in order to free some
Hello Rui,
The problem here is that flexbar repository on the main Galaxy Tool Shed does
not define a relationship between the flexbar tool contained within the
repository and a recipe for installing the flexbar binary dependency. The
flexbar tool config includes the following requirements tag
