From 9bef489d9a5c2fb411c8cecc6166ad6c08b714ca Mon Sep 17 00:00:00 2001 From: Ryan Richholt Date: Tue, 28 Aug 2018 12:12:21 -0700 Subject: [PATCH 1/2] Moved scripts to inst/, made them executable --- {scripts => inst/bin}/createPanelOfNormals.R | 0 {scripts => inst/bin}/runIchorCNA.R | 0 {scripts => inst/scripts}/README.md | 0 {scripts => inst/scripts}/example_gw_plot.png | Bin {scripts => inst/scripts}/snakemake/README.md | 0 .../scripts}/snakemake/config/cluster.sh | 0 .../scripts}/snakemake/config/config.yaml | 0 .../scripts}/snakemake/config/config_hg38.yaml | 0 .../scripts}/snakemake/config/samples.yaml | 0 .../scripts}/snakemake/ichorCNA.snakefile | 0 10 files changed, 0 insertions(+), 0 deletions(-) rename {scripts => inst/bin}/createPanelOfNormals.R (100%) mode change 100644 => 100755 rename {scripts => inst/bin}/runIchorCNA.R (100%) mode change 100644 => 100755 rename {scripts => inst/scripts}/README.md (100%) rename {scripts => inst/scripts}/example_gw_plot.png (100%) rename {scripts => inst/scripts}/snakemake/README.md (100%) rename {scripts => inst/scripts}/snakemake/config/cluster.sh (100%) rename {scripts => inst/scripts}/snakemake/config/config.yaml (100%) rename {scripts => inst/scripts}/snakemake/config/config_hg38.yaml (100%) rename {scripts => inst/scripts}/snakemake/config/samples.yaml (100%) rename {scripts => inst/scripts}/snakemake/ichorCNA.snakefile (100%) diff --git a/scripts/createPanelOfNormals.R b/inst/bin/createPanelOfNormals.R old mode 100644 new mode 100755 similarity index 100% rename from scripts/createPanelOfNormals.R rename to inst/bin/createPanelOfNormals.R diff --git a/scripts/runIchorCNA.R b/inst/bin/runIchorCNA.R old mode 100644 new mode 100755 similarity index 100% rename from scripts/runIchorCNA.R rename to inst/bin/runIchorCNA.R diff --git a/scripts/README.md b/inst/scripts/README.md similarity index 100% rename from scripts/README.md rename to inst/scripts/README.md diff --git a/scripts/example_gw_plot.png b/inst/scripts/example_gw_plot.png similarity index 100% rename from scripts/example_gw_plot.png rename to inst/scripts/example_gw_plot.png diff --git a/scripts/snakemake/README.md b/inst/scripts/snakemake/README.md similarity index 100% rename from scripts/snakemake/README.md rename to inst/scripts/snakemake/README.md diff --git a/scripts/snakemake/config/cluster.sh b/inst/scripts/snakemake/config/cluster.sh similarity index 100% rename from scripts/snakemake/config/cluster.sh rename to inst/scripts/snakemake/config/cluster.sh diff --git a/scripts/snakemake/config/config.yaml b/inst/scripts/snakemake/config/config.yaml similarity index 100% rename from scripts/snakemake/config/config.yaml rename to inst/scripts/snakemake/config/config.yaml diff --git a/scripts/snakemake/config/config_hg38.yaml b/inst/scripts/snakemake/config/config_hg38.yaml similarity index 100% rename from scripts/snakemake/config/config_hg38.yaml rename to inst/scripts/snakemake/config/config_hg38.yaml diff --git a/scripts/snakemake/config/samples.yaml b/inst/scripts/snakemake/config/samples.yaml similarity index 100% rename from scripts/snakemake/config/samples.yaml rename to inst/scripts/snakemake/config/samples.yaml diff --git a/scripts/snakemake/ichorCNA.snakefile b/inst/scripts/snakemake/ichorCNA.snakefile similarity index 100% rename from scripts/snakemake/ichorCNA.snakefile rename to inst/scripts/snakemake/ichorCNA.snakefile From b154df1c9c4ffdcdaca3e01643ebb972f6f16653 Mon Sep 17 00:00:00 2001 From: Ryan Richholt Date: Tue, 28 Aug 2018 12:13:34 -0700 Subject: [PATCH 2/2] Added shebang to scripts so they can be executable --- inst/bin/createPanelOfNormals.R | 1 + inst/bin/runIchorCNA.R | 1 + 2 files changed, 2 insertions(+) diff --git a/inst/bin/createPanelOfNormals.R b/inst/bin/createPanelOfNormals.R index ccea1f5..68366cb 100755 --- a/inst/bin/createPanelOfNormals.R +++ b/inst/bin/createPanelOfNormals.R @@ -1,3 +1,4 @@ +#!/usr/bin/env Rscript library(HMMcopy) library(optparse) library(ichorCNA) diff --git a/inst/bin/runIchorCNA.R b/inst/bin/runIchorCNA.R index f9a99db..d61edc5 100755 --- a/inst/bin/runIchorCNA.R +++ b/inst/bin/runIchorCNA.R @@ -1,3 +1,4 @@ +#!/usr/bin/env Rscript # file: ichorCNA.R # author: Gavin Ha, Ph.D. # Dana-Farber Cancer Institute