Merge pull request #29 from broadinstitute/kv_scripts_cleanup

Changed path to include scripts directory, added Python 2 note

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.
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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>```
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+```./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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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:

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>```
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+```./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>```
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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>```
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+```./run.sh scripts/import_large_tsv/import_large_tsv.py -p <workspace project> -n <workspace name> -f <tsv file name>```
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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"}```
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+```./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"}```
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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>```

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\>
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+* 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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