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David Hoksza
bh19-rare-diseases
Commits
fb98b1a6
Commit
fb98b1a6
authored
Dec 05, 2019
by
David Hoksza
Browse files
readme update
parent
ee256c1a
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1
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README.md
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fb98b1a6
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@@ -22,16 +22,19 @@ pip3 install -r dependencies/python_requirements.txt
##### Java
Maven needs to be installed if you want to compile the
`map_generator`
from the code. This might not be
necesarry, since we provide a compiled version with the code as well. By default the compilation is not
carried out. This can be changed by setting the value
`BUILD_MAP_GENERATOR`
in
`parameters.sh`
to 1.
The maven can be installed on Ubuntu via apt (
`sudo apt install maven`
).
If you want to compile the
`map_generator`
from the code you need Maven (Java package manager) to be installed on your machine.
Maven can be installed on Ubuntu via apt (
`sudo apt install maven`
).
However, this should not be necesarry, as the latest compiled version is shipped with the pipeline.
By default the compilation is not turned on. This can be changed by setting
the value
`BUILD_MAP_GENERATOR`
in
`parameters.sh`
to 1.
##### R
The R scripts
in
the pipeline should be able to install their dependencies on the first run. However,
it might happen that elevated privileges will be needed. If that is the case and the pipeline fail
e
s
on the R scripts, you can install the dependencies by running:
The R scripts
which are part of
the pipeline should be able to install their dependencies on the first run. However,
it might happen that elevated privileges will be needed. If that is the case and the pipeline fails
on the R scripts
execution
, you can install the dependencies by running:
```
bash
sudo
Rscript
--vanilla
dependencies/dependencies.R
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...
@@ -39,7 +42,7 @@ sudo Rscript --vanilla dependencies/dependencies.R
##### System
If the pipeline is run a
t
clean Linux installation you might need to install the following libraries
If the pipeline is run
on
a clean Linux installation you might need to install the following libraries
(
`sudo apt-get install`
on Ubuntu) prior to running the code:
-
libcurl
-
libssl-dev
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