PROFILE -> AWS_PROFILE in both ewings and wilms setup code

AlexsLemonade · Dec 2, 2024 · 3e96b83 · 3e96b83
1 parent 6422de7
commit 3e96b83
Show file tree

Hide file tree

Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/scRNA-seq-advanced/setup/ewing-sarcoma/README.md b/scRNA-seq-advanced/setup/ewing-sarcoma/README.md
@@ -2,12 +2,12 @@ The shell script in this directory downloads processed `SingleCellExperiment` ob
 
 You may want to run it with your OpenScPCA conda environment activated.
 
-By default, it will use an AWS profile called `openscpca` and download data from the `2024-11-25` OpenScPCA release.
+By default, it will use your currently active AWS profile (falling back to one called `openscpca` if not set) and download data from the `2024-11-25` OpenScPCA release.
 
 You can alter the AWS profile or release with the following:
 
 ```sh
-PROFILE={profile} RELEASE={release} ./download-openscpca-data.sh
+AWS_PROFILE={profile} RELEASE={release} ./download-openscpca-data.sh
 ```
 
 Replacing `{profile}` and `{release}` with a profile with OpenScPCA access and valid release, respectively.
diff --git a/scRNA-seq-advanced/setup/ewing-sarcoma/download-openscpca-data.sh b/scRNA-seq-advanced/setup/ewing-sarcoma/download-openscpca-data.sh
@@ -2,8 +2,8 @@
 
 set -euo pipefail
 
-# Profile to use with the download script
-PROFILE=${PROFILE:-openscpca}
+# AWS profile to use with the download script
+AWS_PROFILE=${AWS_PROFILE:-openscpca}
 # Release to download
 RELEASE=${RELEASE:-2024-11-25}
 
@@ -31,15 +31,15 @@ chmod +x download-data.py
     --format SCE \
     --release ${RELEASE} \
     --data-dir ${ewing_data_dir} \
-    --profile ${PROFILE}
+    --profile ${AWS_PROFILE}
 
 # # Download Ewing sarcoma metadata
 ./download-data.py \
     --projects SCPCP000015 \
     --metadata-only \
     --release ${RELEASE} \
     --data-dir ${ewing_data_dir} \
-    --profile ${PROFILE}
+    --profile ${AWS_PROFILE}
 
 # Remove existing files from processed directory
 if [ -z "$( ls -A ${processed_dir} )" ]; then

diff --git a/scRNA-seq-advanced/setup/wilms-tumor/download-openscpca-data.sh b/scRNA-seq-advanced/setup/wilms-tumor/download-openscpca-data.sh
@@ -2,8 +2,8 @@
 
 set -euo pipefail
 
-# Profile to use with the download script
-PROFILE=${AWS_PROFILE:-openscpca}
+# AWS profile to use with the download script
+AWS_PROFILE=${AWS_PROFILE:-openscpca}
 # Release to download
 RELEASE=${RELEASE:-2024-11-25}
 
@@ -32,7 +32,7 @@ chmod +x download-data.py
     --format SCE \
     --release ${RELEASE} \
     --data-dir ${wilms_data_dir} \
-    --profile ${PROFILE}
+    --profile ${AWS_PROFILE}
 
 # Remove existing files from processed directory
 if [ -z "$( ls -A ${processed_dir} )" ]; then
@@ -47,4 +47,4 @@ mv ${wilms_data_dir}/${RELEASE}/${project_id}/* ${processed_dir}
 # Clean up download data script
 rm download-data.py
 # Clean up the remnants of download structure
-rm -r ${wilms_data_dir}/${RELEASE}
+rm -r ${wilms_data_dir}/${AWS_PROFILE}