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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2018-11-25 16:17:36 +0000
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2018-11-25 16:17:36 +0000
commit544752fe2d74da658c94e43cfc45506d17c7d1bb (patch)
tree1b7c0c2bb1ca9b680bacfdd5391fcdacae17ba86
parente623102768c426e86b0ed73904168006dfea2af9 (diff)
Instructions on changing input dataset in pipeline
A step has been added to the checklist to correct the template's input dataset into the custom dataset necessary for each research.
-rw-r--r--README-pipeline.md16
1 files changed, 11 insertions, 5 deletions
diff --git a/README-pipeline.md b/README-pipeline.md
index 6effa30..9ca0cd2 100644
--- a/README-pipeline.md
+++ b/README-pipeline.md
@@ -531,14 +531,20 @@ advanced in later stages of your work.
through the `reproduce/config/pipeline/INPUTS.mk` file. It is best to
gather all the information regarding all the input datasets into this
one central file. To ensure that the proper dataset is being
- downloaded and used by the pipeline, its best to also get an MD5
- checksum (https://en.wikipedia.org/wiki/MD5) of the file and include
- that in thsi file so you can check it in the pipeline. The preparation
- of the input datasets is done in
+ downloaded and used by the pipeline, it is also recommended get an
+ [MD5 checksum](https://en.wikipedia.org/wiki/MD5) of the file and
+ include that in `INPUTS.mk` so you can check it in the pipeline. The
+ preparation of the input datasets is done in
`reproduce/src/make/download.mk`. Have a look there to see how these
values are to be used. This information about the input datasets is
also used in the initial `configure` script (to inform the users), so
- also modify that file.
+ also modify that file. You can find all occurrences of the template
+ dataset with the command below and replace it with your input's
+ dataset.
+
+ ```shell
+ $ grep -ir wfpc2 ./*
+ ```
- **Delete dummy parts (can be done later)**: The template pipeline
contains some parts that are only for the initial/test run, mainly as