From a1e0d58d5a24aa2de47e1b119b2ba22c7f2c38d3 Mon Sep 17 00:00:00 2001
From: MalinAhlberg <malin.ahlberg@nbis.se>
Date: Tue, 16 Apr 2024 14:38:12 +0200
Subject: [PATCH] fix: update start up scripts

---
 scripts/load_data.sh        | 7 -------
 scripts/make_credentials.sh | 8 +-------
 2 files changed, 1 insertion(+), 14 deletions(-)

diff --git a/scripts/load_data.sh b/scripts/load_data.sh
index 7894121..6b96a4c 100644
--- a/scripts/load_data.sh
+++ b/scripts/load_data.sh
@@ -7,15 +7,8 @@ pip -q install s3cmd
 
 FILES="htsnexus_test_NA12878.bam htsnexus_test_NA12878.bam.bai htsnexus_test_NA12878.bam.blocks.yaml htsnexus_test_NA12878.bam.gzi"
 for file in ${FILES}; do
-    #curl -s -L -o "$file" "https://github.com/ga4gh/htsget-refserver/raw/main/data/gcp/gatk-test-data/wgs_bam/$file"
     curl -s -L -o "$file" "https://github.com/umccr/htsget-rs/raw/main/data/bam/$file"
 
-    #case $file in (*.bai)
-    #    newname="$(basename "$file" .bai).bam.bai"
-    #    mv "$file" "$newname"
-    #    file="$newname"
-    # ;;
-    #esac
 
     yes | /shared/crypt4gh encrypt -p /shared/c4gh.pub.pem -f "$file"
     ENC_SHA=$(sha256sum "$file.c4gh" | cut -d' ' -f 1)
diff --git a/scripts/make_credentials.sh b/scripts/make_credentials.sh
index 1708f73..455cdf0 100644
--- a/scripts/make_credentials.sh
+++ b/scripts/make_credentials.sh
@@ -50,16 +50,10 @@ socket_timeout = 30
 EOD
 
 ## create crypt4gh key
-#if [ ! -f "/shared/c4gh.sec.pem" ]; then
-#    curl -s -L https://github.com/neicnordic/crypt4gh/releases/download/v"${C4GH_VERSION}"/crypt4gh_linux_x86_64.tar.gz | tar -xz -C /shared/ && chmod +x /shared/crypt4gh
-#    /shared/crypt4gh generate -n /shared/c4gh -p c4ghpass
-#fi
 if [ ! -f "/shared/c4gh.sec.pem" ]; then
     curl -s -L https://github.com/neicnordic/crypt4gh/releases/download/v"${C4GH_VERSION}"/crypt4gh_linux_x86_64.tar.gz | tar -xz -C /shared/ && chmod +x /shared/crypt4gh
-#    /shared/crypt4gh generate -n /shared/c4gh -p c4ghpass
+    /shared/crypt4gh generate -n /shared/c4gh -p c4ghpass
 fi
-cp /scripts/c4gh.sec.pem /shared/c4gh.sec.pem
-cp /scripts/c4gh.pub.pem /shared/c4gh.pub.pem
 
 ## create TLS certificates
 bash /scripts/certs/make_certs.sh