There is a README.txt in the pkgs folder.
I will attach it. I think this is accurate, but there may be something
else on the site.
On Thu, Oct 23, 2014 at 10:23 PM, Henrik Bengtsson h...@biostat.ucsf.edu
wrote:
It's been a while since I worked with experimental packages. Where
can I find documentation on how to (Subversion) update our
AffymetrixDataTestFiles package with additional data files? All I
know is that the SVN repository only contains a stub of the package
and
http://www.bioconductor.org/developers/package-guidelines/#package-types
provides little information and basically only point to the devel
mailing list.
Thanks,
Henrik
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BioC Experiment Data Package SVN Repos
:Date: 2006-08-10
:Author: S. Falcon
:svn URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs
Background
==
This svn directory contains BioC experiment data packages. Data
packages contain potentially large binary files that do not change
often. Most updates to these packages involve the package
infrastructure files.
Obtaining a working copy of a data package over a slow connection can
be frustrating, especially when all that is needed is the
infrastructure files and not the actual data. We have implemented a
scheme that allows separate checkout of infrastructure files and data
files. This document describes the scheme and provides instructions
for checkout and update of existing data packages as well as for
adding new packages.
How to Create an Infrastructure-Only Workingcopy
You can obtain a checkout of all experiment data package
infrastructure files as follows::
svn checkout \
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs
To obtain the files for a particular package, say ``ALL``::
svn checkout \
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ALL
If you want to preview what is available, you might try the
following::
# get the top-level scripts, but don't recurse into subdirs
svn checkout -N \
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs
# see what is there
svn ls https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs
# get a particular package's infrastructure files
cd pkgs
svn up ALL
# see next section for getting complete working copy w/ data
How to Create a Complete Workingcopy
First create a workingcopy of the infrastructure files as described
above.
Next use the helper script ``add_data.py`` (you will need Python). It
is located here:
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/add_data.py
Here's a complete example for ``ALL``::
svn checkout \
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ALL
python add_data.py ALL
This will add the big data directories (usually data/, but sometimes
also dirs under inst/) to your working copy. Usually, the svn:ignore
property has been set so that you won't accidentally add these dirs
when working with the package, but please take care anyway.
A note about committing changes to the data
---
If you want to modify the actual data, cd into the appropriate dir
after having run add_data.py and do your commit from there. The
script adds a full working copy inside the infrastructure working
copy.
How to Add a New Data Package
=
1. Add the infrastructure files under ``pkgs``.
2. Add any large data directories to ../data_store/PKGNAME/. For
example, if there is large data in PKGNAME/data and
PKGNAME/inst/extdata, you would add PKGNAME/data and
PKGNAME/inst/extdata to ../data_store.
3. Create a file 'external_data_store.txt' listing each dir that is
stored externally (each on a separate line). Contining the example
above, the file would contain::
data
inst/extdata
This should go in the top-level of the package dir.
4. Add svn ignore properties. Continuing the example::
cd PKGNAME
svn propset svn:ignore '*' ./data/ ## property 'svn:ignore' set on '.'
## in the data folder
svn propset svn:ignore '*' ./inst/
or (this might not work anymore)
svn propedit svn:ignore . ## add 'data' here
svn propedit svn:ignore inst ## add 'extdata' here
5. Commit.
Details of Storage Scheme
=
Experiment data package infrastructure files live in
``experiment/pkgs``. Package subdirectories that contain large files
are stored under ``experiment/data_store``. There is no mechanism to
support separate storage of individual files.
Here is an example of how data for the
