diff options
authorJustin Bedo <cu@cua0.org>2021-02-16 21:18:01 +1100
committerJustin Bedo <cu@cua0.org>2021-02-16 21:18:31 +1100
commit834d736a00f5bd7155cb137d5a3e94e1413e8ada (patch)
parent4f7f2770baecc5f72ca9e90d7996c0a1554bda1b (diff)
Add -I flags to example invocations
BioNix is expected to be in the search path, which by default is not the case. Explicitly adding include flags to the build invocation in the examples simplifies execution for new users (issue #17).
1 files changed, 4 insertions, 3 deletions
diff --git a/examples/README.md b/examples/README.md
index 1689709..b12c172 100644
--- a/examples/README.md
+++ b/examples/README.md
@@ -3,7 +3,8 @@
This directory has a few example workflows in bionix along with example
data. A basic workflow is defined in `call.nix`, and an example of
applying it to the sample data is in `default.nix`. To build the
-`default.nix` workflow, run ```nix build``` from this directory.
+`default.nix` workflow, run ```nix build -I bionix=../``` from this directory.
+Note that the location of BioNix
## NextFlow and WDL translations
@@ -12,12 +13,12 @@ from the NextFlow and WDL documentation respectively.
The NextFlow translated example does not come with example data. It can be built with
-nix build -f nextflow-example1.nix --arg input /path/to/sample.fa
+nix build -f nextflow-example1.nix -I bionix=../.. --arg input /path/to/sample.fa
The WDL example requires no extra data and can be built with
-nix build -f wdl-scatter-gather.nix
+nix build -f wdl-scatter-gather.nix -I bionix=../..
## Example script wrapper