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broadinstitute · Jul 22, 2022 · 3bcf33a · 3bcf33a
1 parent 2a67c6b
commit 3bcf33a
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/build_docker.sh b/build_docker.sh
@@ -91,10 +91,10 @@ if [ -n "$STAGING_DIR" ]; then
     mkdir -p ${STAGING_DIR}
     cd ${STAGING_DIR}
     set +e
-    rm -Rf ${STAGING_DIR}/${STAGING_CLONE_DIR}
+    rm -Rf ${STAGING_CLONE_DIR}
     set -e
     GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/${REPO}/${PROJECT}.git ${STAGING_CLONE_DIR}
-    cd ${STAGING_DIR}/${STAGING_CLONE_DIR}
+    cd ${STAGING_CLONE_DIR}
     STAGING_ABSOLUTE_PATH=$(pwd)
 
     echo "Now in $(pwd)"

diff --git a/build_docker_remote.sh b/build_docker_remote.sh
@@ -31,11 +31,11 @@ done
 
 if [ -z "$GITHUB_TAG" ]; then
 	printf "Option -e requires an argument.\n \
-Usage: %s: -e <GITHUB_TAG> [-psl] \n \
+Usage: %s: -e <GITHUB_TAG> [-sdt] \n \
 where <GITHUB_TAG> is the github tag (or hash when -s is used) to use in building the docker image\n \
 (e.g. bash build_docker_remote.sh -e 4.2.6.1 )\n \
 Optional arguments:  \n \
--s \t The GITHUB_TAG (-e parameter) is actually a github hash, not tag.  git hashes cannot be pushed as latest, so -l is implied.  \n \
+-s \t The GITHUB_TAG (-e parameter) is actually a github hash, not tag.  \n \
 -d <STAGING_DIR> \t staging directory to grab code from repo and build the docker image.  If unspecified, then use whatever is in current dir (do not go to the repo).  NEVER SPECIFY YOUR WORKING DIR \n \
 -t <IMAGE_TAG>\t  The tag to assign image once it is finished constructing.  NOTE: currently this MUST be on either GCR or the Google Artifact Registry. \n" $0
 	exit 1
@@ -44,7 +44,7 @@ fi
 # Output the parameters
 echo -e "\n"
 echo -e "github tag/hash: ${GITHUB_TAG}"
-echo -e "github project: ${REPO_PRJ}:${GITHUB_TAG}\n\n"
+echo -e "github project: ${REPO}/${PROJECT}:${GITHUB_TAG}\n\n"
 echo "Other options (Blank is false)"
 echo "---------------"
 echo "This is a git hash: ${IS_HASH}"
@@ -62,10 +62,10 @@ if [ -n "$STAGING_DIR" ]; then
     mkdir -p ${STAGING_DIR}
     cd ${STAGING_DIR}
     set +e
-    rm -Rf ${STAGING_DIR}/${STAGING_CLONE_DIR}
+    rm -Rf ${STAGING_CLONE_DIR}
     set -e
     GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/${REPO}/${PROJECT}.git ${STAGING_CLONE_DIR}
-    cd ${STAGING_DIR}/${STAGING_CLONE_DIR}
+    cd ${STAGING_CLONE_DIR}
     STAGING_ABSOLUTE_PATH=$(pwd)
 
     echo "Now in $(pwd)"

diff --git a/scripts/docker/README.md b/scripts/docker/README.md
@@ -23,7 +23,7 @@ This repo contains the scripts for creating and pushing two docker images:
 
 ``scripts/docker/gatkbase/build_docker_base.sh`` is a script to create the gatkbase docker image. 
 ``build_docker.sh`` is a script to create the full gatk4 docker image.
-``build_docker_remote.sh`` is a script to create the full gatk4 docker image using google cloud build remotely. This is useful if you can't build the docker image locally (if you have an M1 Macbook) NOTE: this requires the user first specify their project with the command `gcloud config set project <PROJECT>` to a project that has access to google cloud build. 
+``build_docker_remote.sh`` is a script to create the full gatk4 docker image using google cloud build remotely. This is useful if you can't build the docker image locally (for example if you have an M1 Macbook) NOTE: this requires the user first specify their project with the command `gcloud config set project <PROJECT>` to a project that has access to google cloud build. 
 
 ## GATK4 Docker image