diff --git a/scRNA-seq-advanced/setup/ewing-sarcoma/README.md b/scRNA-seq-advanced/setup/ewing-sarcoma/README.md index eb89f84e..a95203a3 100644 --- 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 index 7ccae206..a4f556ac 100755 --- 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} @@ -31,7 +31,7 @@ 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 \ @@ -39,7 +39,7 @@ chmod +x download-data.py --metadata-only \ --release ${RELEASE} \ --data-dir ${ewing_data_dir} \ - --profile ${PROFILE} + --profile ${AWS_PROFILE} # Remove existing files from processed directory if [ -z "$( ls -A ${processed_dir} )" ]; then diff --git a/scRNA-seq-advanced/setup/wilms-tumor/download-openscpca-data.sh b/scRNA-seq-advanced/setup/wilms-tumor/download-openscpca-data.sh index c991c761..3892261f 100755 --- a/scRNA-seq-advanced/setup/wilms-tumor/download-openscpca-data.sh +++ b/scRNA-seq-advanced/setup/wilms-tumor/download-openscpca-data.sh @@ -2,8 +2,8 @@ set -euo pipefail -# Profile to use with the download script -PROFILE=${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}