From 75e4303f65d5c574fbd3a99671dc428f6d28d7aa Mon Sep 17 00:00:00 2001
From: Kate Voss <kvoss@broadinstitute.org>
Date: Thu, 22 Mar 2018 16:17:07 -0400
Subject: [PATCH] Changed path to scripts for run example
---
README.md | 1 +
scripts/add_many_emails_to_method/README.md | 2 +-
scripts/bigquery_billing_report/README.md | 6 +++---
scripts/entity_to_tsv_for_large_data/README.md | 2 +-
scripts/import_large_tsv/README.md | 2 +-
scripts/rebind_output_attributes/README.md | 2 +-
scripts/register_service_account/README.md | 2 +-
scripts/storage_costs_estimates/README.md | 8 ++++++--
8 files changed, 15 insertions(+), 10 deletions(-)
diff --git a/README.md b/README.md
index b355a62..4ebedf2 100644
--- a/README.md
+++ b/README.md
@@ -10,6 +10,7 @@ To run a giving script using Docker:
## Prerequisites
* Install the Google Cloud SDK from https://cloud.google.com/sdk/downloads
* Set the Application Default Credentials (run `gcloud auth application-default login`)
+* Python 2.7
When running without the run script or docker, check the packages that are pip
installed in either run.sh or the Dockerfile.
\ No newline at end of file
diff --git a/scripts/add_many_emails_to_method/README.md b/scripts/add_many_emails_to_method/README.md
index 986f4de..507327f 100644
--- a/scripts/add_many_emails_to_method/README.md
+++ b/scripts/add_many_emails_to_method/README.md
@@ -2,4 +2,4 @@
This script takes in a file of email addresses (one per line) and uses those to set permissions on a given method or config. All users in that file will get the same access level, so if other access levels are needed per "group" of users, you must use different files.
Run this as follows (from the main directory):
-```./run.sh add_many_emails_to_method/add_many_emails_to_method.py -s <method/config namespace> -n <method/config name> -i <snapshot id> -t <type, either method or config> -r <access level, either READER or OWNER> -f <file with one email per line>```
\ No newline at end of file
+```./run.sh scripts/add_many_emails_to_method/add_many_emails_to_method.py -s <method/config namespace> -n <method/config name> -i <snapshot id> -t <type, either method or config> -r <access level, either READER or OWNER> -f <file with one email per line>```
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diff --git a/scripts/bigquery_billing_report/README.md b/scripts/bigquery_billing_report/README.md
index b5e6a38..66e2dfb 100644
--- a/scripts/bigquery_billing_report/README.md
+++ b/scripts/bigquery_billing_report/README.md
@@ -3,9 +3,9 @@ This script will provide a cost breakdown for either (a) all workflows in all su
Usage:
-* All submissions in a workspace: ./run.sh bigquery_billing_report/bigquery_billing_report.py -p \<firecloud billing project name\> -n \<workspace name\>
-* All workflows in a submission: ./run.sh bigquery_billing_report/bigquery_billing_report.py -p \<firecloud billing project name\> -n \<workspace name\> -s \<submission id\>
-* A single workflow: ./run.sh bigquery_billing_report/bigquery_billing_report.py -p \<firecloud billing project name\> -n \<workspace name\> -s \<submission id\> -w \<workflow id\>
+* All submissions in a workspace: ./run.sh scripts/bigquery_billing_report/bigquery_billing_report.py -p \<firecloud billing project name\> -n \<workspace name\>
+* All workflows in a submission: ./run.sh scripts/bigquery_billing_report/bigquery_billing_report.py -p \<firecloud billing project name\> -n \<workspace name\> -s \<submission id\>
+* A single workflow: ./run.sh scripts/bigquery_billing_report/bigquery_billing_report.py -p \<firecloud billing project name\> -n \<workspace name\> -s \<submission id\> -w \<workflow id\>
* For Big Query datasets not exported to the firecloud billing project:
diff --git a/scripts/entity_to_tsv_for_large_data/README.md b/scripts/entity_to_tsv_for_large_data/README.md
index 01a361a..e1e2eca 100644
--- a/scripts/entity_to_tsv_for_large_data/README.md
+++ b/scripts/entity_to_tsv_for_large_data/README.md
@@ -2,4 +2,4 @@
This script writes a TSV file for a given entity when that entity is too large to download from the GUI.
Run this as follows (from the main directory):
-```./run.sh entity_to_tsv_for_large_data/entity_to_tsv_for_large_data.py -p <workspace project> -n <workspace name> -e <entity type, e.g. sample> -o <output_tsv_file_name>```
\ No newline at end of file
+```./run.sh scripts/entity_to_tsv_for_large_data/entity_to_tsv_for_large_data.py -p <workspace project> -n <workspace name> -e <entity type, e.g. sample> -o <output_tsv_file_name>```
\ No newline at end of file
diff --git a/scripts/import_large_tsv/README.md b/scripts/import_large_tsv/README.md
index faaa889..e5d82fe 100644
--- a/scripts/import_large_tsv/README.md
+++ b/scripts/import_large_tsv/README.md
@@ -2,4 +2,4 @@
This script imports a TSV file when it is too large to import from the GUI.
Run this as follows (from the main directory):
-```./run.sh import_large_tsv/import_large_tsv.py -p <workspace project> -n <workspace name> -f <tsv file name>```
\ No newline at end of file
+```./run.sh scripts/import_large_tsv/import_large_tsv.py -p <workspace project> -n <workspace name> -f <tsv file name>```
\ No newline at end of file
diff --git a/scripts/rebind_output_attributes/README.md b/scripts/rebind_output_attributes/README.md
index 62f5872..9f5d58a 100644
--- a/scripts/rebind_output_attributes/README.md
+++ b/scripts/rebind_output_attributes/README.md
@@ -4,4 +4,4 @@ This script will take a submission id from a given workspace and bind the output
Optionally an expression override argument can be given that allows new output expressions to be defined and override the existing method config's output expressions. This can be used for example to bind an output that did not originally have an expresion defined for it when the analysis was run.
Run this as follows (from the main directory):
-```./run.sh rebind_output_attributes/rebind_output_attributes.py -p <workspace project> -n <workspace name> -s <submission id of the overriding outputs> -e <optional, if used this can override output expressions used in the method config for this submission. Syntax is in the form {"output_name": "expression"}```
\ No newline at end of file
+```./run.sh scripts/rebind_output_attributes/rebind_output_attributes.py -p <workspace project> -n <workspace name> -s <submission id of the overriding outputs> -e <optional, if used this can override output expressions used in the method config for this submission. Syntax is in the form {"output_name": "expression"}```
\ No newline at end of file
diff --git a/scripts/register_service_account/README.md b/scripts/register_service_account/README.md
index 34dffac..54f759d 100644
--- a/scripts/register_service_account/README.md
+++ b/scripts/register_service_account/README.md
@@ -5,4 +5,4 @@ In order to run this script you will need to download the credentials JSON file
Usage (from the main directory where run.sh resides):
-```./run.sh register_service_account/register_service_account.py -j <path to your service account credentials json file> -e <email address for owner of this service account>```
+```./run.sh scripts/register_service_account/register_service_account.py -j <path to your service account credentials json file> -e <email address for owner of this service account>```
diff --git a/scripts/storage_costs_estimates/README.md b/scripts/storage_costs_estimates/README.md
index 0553f11..4048307 100644
--- a/scripts/storage_costs_estimates/README.md
+++ b/scripts/storage_costs_estimates/README.md
@@ -3,5 +3,9 @@ This script will display the estimated storage costs for a single workspace or a
Usage:
-* All workspaces in a project: ./run.sh storage_costs_estimates/storage_costs_estimates.py -p \<firecloud billing project name\>
-* A single workspace: ./run.sh storage_costs_estimates/storage_costs_estimates.py -p \<firecloud billing project name\> -n \<workspace name\>
\ No newline at end of file
+* All workspaces in a project:
+ ./run.sh scripts/storage_costs_estimates/storage_costs_estimates.py -p \<firecloud billing project name\>
+* A single workspace:
+ ./run.sh scripts/storage_costs_estimates/storage_costs_estimates.py -p \<firecloud billing project name\> -n \<workspace name\>
+
+You can find the [FireCloud billing project name here](https://portal.firecloud.org/#billing) and the [workspace name here](https://portal.firecloud.org/#workspaces).
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--
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