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Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.
Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.
Also, some of the software versions were also updated after some checks
with their webpages.
This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).
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All occurances of "pipeline" have been chanaged to "project" or "template"
withint the text (comments, READMEs, and comments) of the template. The
main template branch is now also named `template'.
This was all because `pipeline' is too generic and couldn't be
distinguished from the base, and customized project.
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Until now, the files where the people were meant to change didn't have a
proper copyright notice (for example `Copyright (C) YOUR NAME.'). This was
wrong because the license does not convey copyright ownership. So the name
of the file's original author must always be included and when people
modify it (and add their own copyright-able modifications).
With this commit, the file's original author (and email) are added to the
copyright notice and when more than one person modified a file, both names
have their individual copyright notice.
Based on this, the description for adding a copyright notice in
`README-hacking.md' has also been modified.
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Until now, we were using `flock' (file-lock) for downloading the input
datasets in series. But we couldn't do this when downloading the software
tarballs because `flock' wasn't yet available. Generally, unlike
processing, downloading is much better done in series than in parallel.
To enable serial downloads of the software also, with this commit we are
installing `flock' in the configure script (not in a Makefile). As a
result, besides `flock', we can also benefit from the other good features
of the `reproduce/src/bash/download-multi-try' script *(for example
attempting download again after some time).
Some GNU mirrors may have problems at the time of download, so with this
commit, we are using the main GNU FTP server for GNU programs.
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In the example running code of the wrapper script, I had just written
`./download-multi-try', but this script is meant to be run from the top of
the project directory. This could cause confusion.
So the example script now starts with `/path/to/download-multi-try'.
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We don't have a `.sh' suffix in the other scripts of `reproduce/src/bash',
so it was also removed from this script.
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