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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2018-02-19 18:18:49 +0100
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2018-02-19 18:18:49 +0100
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parentf82fcdb601c24db4d04823edb26965cec9b0818a (diff)
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A few other minor corrections were applied to the text to be more clear.
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@@ -245,9 +245,7 @@ been explained here), please let us know to correct it.
- **Start your exciting research**: You are now ready to add flesh and
blood to this raw skeleton by further modifying and adding your
- exciting research steps. Just don't forget to share your experiences
- with us as you go along so we can make this a more robust
- skeleton. You can see some published pipelines in
+ exciting research steps. You can see some published pipelines in
[zenodo.1163746](https://doi.org/10.5281/zenodo.1163746) and
[zenodo.1164774](https://doi.org/10.5281/zenodo.1164774). The
reproduction pipeline tarball names follow this format
@@ -257,6 +255,14 @@ been explained here), please let us know to correct it.
pipeline of the respective project.
+ - **Feedback**: As you use the pipeline you will notice many things that
+ if implemented from the start would have been very useful for your
+ work. This can be in the actual file structure of the pipeline or in
+ useful implementation and usage tips like below. In any case, since
+ this concept is still evolving, please share your thoughts and
+ suggestions, so we can add them here for everyone's benefit.
+
+
@@ -388,7 +394,7 @@ us. In this way, we can add it here for the benefit of others.
rm $(subst .txt,,$<)
echo "done" > $@
```
- A more advanced Make programmer will use [Make's call
+ A more advanced Make programmer will use Make's [call
function](https://www.gnu.org/software/make/manual/html_node/Call-Function.html)
to define a wrapper in `reproduce/src/make/initialize.mk`. This
wrapper will replace `$(subst .txt,,XXXXX)`. Therefore, it will be
@@ -407,11 +413,14 @@ us. In this way, we can add it here for the benefit of others.
higher-level libraries they depend on). Software evolves very fast
and only in a few years, a feature might be changed or removed from
the mainstream version or the software server might go down. To be
- safe, keep a copy of the tarballs (they are hardly ever over a few
- megabytes, very insignificant compared to the data). If you intend to
- release the pipeline in a place like Zenodo, then you can create your
- submission early (before public release) and upload/keep all the
- necessary tarballs (and data) there.
+ safe, keep a copy of the tarballs. Software tarballs are rarely over
+ a few megabytes, very insignificant compared to the data. If you
+ intend to release the pipeline in a place like Zenodo, then you can
+ create your submission early (before public release) and upload/keep
+ all the necessary tarballs (and data)
+ there. [zenodo.1163746](https://doi.org/10.5281/zenodo.1163746) is
+ one example of how the data, Gnuastro (main software used) and all
+ major Gnuastro's dependencies have been uploaded with the pipeline.
- *Keep your input data*: The input data is also critical to the
pipeline, so like the above for software, make sure you have a backup