Complete, end-user control over how and where Galaxy reads and writes
files would be particularly useful for dealing with very large files and
for integrating Galaxy output into complex, ad hoc external workflows.
I have three suggestions:
1. Rename the "Upload File" tool as "Data Source" and allow users
to
select whether the specified file should be uploaded to "Galaxy" or read
in situ.
2. Create a new tool called "Default Data Destination" with which
users can specify the default path where all data output is to be written.
3. Add a "Data Destination" field to the page of every tool that
writes output to disk, so users can specify, on a tool-by-tool basis,
where they want the output to be written.
a. If the user has specified a default location via the "Default
Data Destination" tool, the field would be pre-filled with this path;
b. if not, the field would be blank (or contain "to Galaxy" in
disabled text), and Galaxy will write to its write folder,
c. unless the user explicitly specifies a new write path in this
field for this tool.
I am aware of the various, current ways one can specify file handling
strategies within Galaxy, but these seem to be too static, too global,
and too "subliminal" for the kind of work at hand; something finer-
grained, more pervasive, and more explicit seems to be called for.
[If implemented, it is clear that these changes would add fragility to
the Galaxy history mechanism, but this could be dealt with at multiple
levels, including in the UI by issuing warnings and/or offering choices.]
Thanks for all your great work on this fine platform for tool
integration. (In the words of one of your very knowledgeable
"competitors" on seeing Galaxy for the first time, "This is slick!" )
Dean A. Snyder
Senior Programmer/Analyst
Center for Inherited Disease Research (CIDR)
Johns Hopkins School of Medicine
Bayview Research Campus
333 Cassell Dr, Triad Bldg, Suite 2000
Baltimore, MD 21224
www.cidr.jhmi.edu
cell:717 668-3048 office:410-550-4629