diff --git a/README.md b/README.md
index b355a62e660c829da0e37090aa9b622e69a3d681..4ebedf2ffa6fc6eb542b72168672968d64a7407f 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.
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diff --git a/scripts/add_many_emails_to_method/README.md b/scripts/add_many_emails_to_method/README.md
index 986f4decb27fe1cd47f8a452f0cc182bf2a88868..507327fe489ee3baeebd9362ca001e924f5e929c 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>```
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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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diff --git a/scripts/bigquery_billing_report/README.md b/scripts/bigquery_billing_report/README.md
index b5e6a387fc27cf5acd6a23597ddaf0f58922eddc..66e2dfb0fb88d12f8a2d208e166f9b588e473136 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 01a361a84841f4087d028f6faed1837ed471af49..e1e2ecab1dc14fa1723f3e9e92c4949d8aad1155 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>```
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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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diff --git a/scripts/import_large_tsv/README.md b/scripts/import_large_tsv/README.md
index faaa8897f22885fdcce01b59872801b0858db8cd..e5d82feb85c7eb2c26c2bf1e62b0938ecbd0e29d 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>```
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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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diff --git a/scripts/rebind_output_attributes/README.md b/scripts/rebind_output_attributes/README.md
index 62f587271f2673f636c2f28b727edeb1f2da8975..9f5d58ab4a2723a79b0c325226ec4205b9d81c83 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"}```
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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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diff --git a/scripts/register_service_account/README.md b/scripts/register_service_account/README.md
index 34dffacb40b28c0fb040d7262b2f3312eb17f1a8..54f759db0779edaa532a386e24e29b813083ab1b 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 0553f117deb0c714804fba87e2054f8e56c0fcc8..40483078b0644946d20fdccaee0491d1758c4db8 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\>
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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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