From f21104afffe7a5cb28f7824211f90dc778d45b57 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Mon, 19 Feb 2018 18:18:49 +0100 Subject: Minor edits in README.md A few other minor corrections were applied to the text to be more clear. --- README.md | 27 ++++++++++++++++++--------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 832cee1..11050c4 100644 --- a/README.md +++ b/README.md @@ -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 -- cgit v1.2.1