Hello Pieter,
Please make sure to address items like this to the galaxy-dev@lists.bx.psu.edu
mailing list rather than individual email accounts as that will ensure more
timely responses that include more optimal feedback.
Sanitizing values from input text fields on tools and other Galaxy forms
Hi,
I am currently trying to use ProtK on our Galaxy installation. I have finally
installed successfully ProtK on our sever by:
rvm install 1.9.3 --with-gcc=clang
rvm use 1.9.3
gem install protk
So, I can see all the *.rb file in the bin folder
(/home/base/.rvm/gems/gems/protk-1.2.5/bin/).
We
Hi @ all,
I would like to know if anyone could give me some guidance or hint on
how to migrate data 'correctly' if Galaxy already wrote files, worked on
the database etc.
The situation is that we set up an instance, it was already in use and
wrote files e.g. into the directory
Hi John,
Thansk for the feedback. Righto, I saw abundant use of trans in core galaxy
code; and problem is I'd wanted access from a tool wrapper's python code.
Basically I'm trying to get more out of .loc files, for example this field
specification for blast report data:
#value type
To whom it may concern,
I am a grad student at the University of Iowa using Galaxy to analyze data from
an RNA-seq experiment. I have been using Tophat2 and noticed that it is not
longer providing an alignment summary text file in the output, which it used to
do. I was wondering if this was an
A colleague has asked me to set up a galaxy server for purpose of running
tophat/cufflinks.
A recent paper in BMC Genomics would indicate that those tools are integrated
into Galaxy.
When I download (hg clone) the distribution, I only see tophat, but none of the
other tuxedo software. The
Brandi,
The cufflinks tools are now available on the main Galaxy tool shed:
http://toolshed.g2.bx.psu.edu/view/devteam/all_cufflinks_tool_suite
Installing this repository into your Galaxy instance will pull in the
versions of the tools that were originally distributed with the Galaxy
