I tried to install ng-chm. I have done all the steps described
in that manual. But when I generate the heat map, I am not getting a menu
for visualization in galaxy and still the path is shown as /shed_tool/....
in my home directory not /galaxy/config.
I have moved the zipped heat map into the visualization folder inside
plugin. And unzipped there itself. But the path is not taking.
Aswathy Mary Paul
Computational biology and Bioinformatics
Cancer Research Program [CRP-9]
Rajiv Gandhi Center for Biotechnology
Thiruvananthapuram-695014, Kerala, lab extn : 247
My Google-Fu is failing me...
We have a visualization plugin that can also serve as an editor to modify the data it is visualizing. What is the best way to save the data from the visualizer back to Galaxy?
So two questions:
1. Is the upload tool (still) the recommended way to put data into the current history via API calls?
Department of Computer Science
Vassar College, Poughkeepsie NY
I'm working on galaxy integration for an MLST tool called MentaLiST:
I've created data managers that create kmer databases and store their
locations in a Tool Data Table. I'd like to allow users to remove entries
from the Tool Data Table. Has anyone seen a Data Manager that provides that
functionality? Should I create separate data managers for add and remove
functionality, or can it be integrated into one?
I'm currently solving a problem with authentication to FTP service for users of
our galaxy server. We've successfully established an authentication via
shibboleth behind Nginx (not very easy, but doable :) but that also means that
ProFTPD is not working anymore, as it doesn't support SAML authentication.
So my question is obvious, I'm looking for an easy and free FTP server with
SAML support, can anybody help me with an advice? I've already found
CompleteFTP and CrushFTP but both are paid and one is Windows-only allegedly.
So how do you - people using external authentication via SAML - do
Thanks in advance for any kind of useful advice.
I am having a problem using planemo to upload a suite of tools into the testtoolshed. The tools at this point are all in the toolshed from using the shed_create and shed_update commands in the suite directory. However, along the way there were some errors in uploading some of the tools that I had to fix. Those are all fixed and all the tools show as up to date, except for the suite, which is returning the following error message, about which I have no idea what to do (and I have tried a lot of different things):
The repository_dependencies.xml file contains an invalid <repository> tag. Invalid latest installable changeset_revision 000000000000 retrieved for repository ctat_metagenomics owned by trinity_ctat.
Does anyone have an idea of what to do to fix this?
I am trying to upload files via FTP. However, the following message appears.
"Authentication required ftp://usegalaxy.org Your connection to this site
is not private." I do not have the experience to use galaxy, What I need to
I would appreciate your advice regarding the recommended portable computer specifications which will enable running the GALXY software for analysis of DNA and RNA seq of bacterial genomes.
I'm trying to install Ballgown but it throws some error message after
cannot find 'dataset' while searching for 'param_name.dataset.dataset'
the script does not have test-data file and it also does not install the