refactor: change more image references to ghcr.io

biorack · Oct 16, 2023 · 8e51116 · 8e51116
1 parent ee30837
commit 8e51116
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Showing 10 changed files with 10 additions and 10 deletions.
diff --git a/metatlas/scripts/copy_ms_to_new_names.sh b/metatlas/scripts/copy_ms_to_new_names.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-shifter -e PYTHONPATH=/src --image=doejgi/metatlas_shifter:latest python /src/metatlas/scripts/copy_ms_to_new_names.py $@
+shifter -e PYTHONPATH=/src --image=ghcr.io/biorack/metatlas/metatlas_shifter:latest python /src/metatlas/scripts/copy_ms_to_new_names.py $@
diff --git a/metatlas/scripts/run_file_converter.sh b/metatlas/scripts/run_file_converter.sh
@@ -27,7 +27,7 @@ LOGFILE="/global/cfs/cdirs/m2650/file_converter_logs/file_converter.log"
 RAW_DATA_PATH=/global/cfs/cdirs/metatlas/raw_data
 
 # pass in PYTHONPATH and don't use "--entrypoint" so that it doesn't copy the git repo to /tmp/metatlas.*
-BIN_PATH="shifter -e PYTHONPATH=/src --image=doejgi/metatlas_shifter:latest /usr/local/bin/python"
+BIN_PATH="shifter -e PYTHONPATH=/src --image=ghcr.io/biorack/metatlas/metatlas_shifter:latest /usr/local/bin/python"
 
 $BIN_PATH -m metatlas.io.file_converter "$RAW_DATA_PATH" &>> "${LOGFILE}" &
 

diff --git a/notebooks/reference/Add_Atlas_to_DB.ipynb b/notebooks/reference/Add_Atlas_to_DB.ipynb
@@ -72,7 +72,7 @@
     "\n",
     "\n",
     "logger = logging.getLogger(\"metatlas.jupyter\")\n",
-    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=doejgi/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
+    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=ghcr.io/biorack/metatlas/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
     "                 \"ipykernel_launcher\",\"-f\",\"{connection_file}\"],\"display_name\": \"Metatlas Targeted\",\"language\": \"python\",\n",
     "                 \"metadata\": { \"debugger\": true }}\"\"\"\n",
     "kernel_file_name = Path.home() / \".local\" / \"share\" / \"jupyter\" / \"kernels\" / \"metatlas-targeted\" / \"kernel.json\"\n",

diff --git a/notebooks/reference/Add_MSMS_Reference.ipynb b/notebooks/reference/Add_MSMS_Reference.ipynb
@@ -62,7 +62,7 @@
     "\n",
     "\n",
     "logger = logging.getLogger(\"metatlas.jupyter\")\n",
-    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=doejgi/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
+    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=ghcr.io/biorack/metatlas/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
     "                 \"ipykernel_launcher\",\"-f\",\"{connection_file}\"],\"display_name\": \"Metatlas Targeted\",\"language\": \"python\",\n",
     "                 \"metadata\": { \"debugger\": true }}\"\"\"\n",
     "kernel_file_name = Path.home() / \".local\" / \"share\" / \"jupyter\" / \"kernels\" / \"metatlas-targeted\" / \"kernel.json\"\n",

diff --git a/notebooks/reference/RT-Alignment.ipynb b/notebooks/reference/RT-Alignment.ipynb
@@ -198,7 +198,7 @@
     "\n",
     "\n",
     "logger = logging.getLogger(\"metatlas.jupyter\")\n",
-    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=doejgi/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
+    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=ghcr.io/biorack/metatlas/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
     "                 \"ipykernel_launcher\",\"-f\",\"{connection_file}\"],\"display_name\": \"Metatlas Targeted\",\"language\": \"python\",\n",
     "                 \"metadata\": { \"debugger\": true }}\"\"\"\n",
     "kernel_file_name = Path.home() / \".local\" / \"share\" / \"jupyter\" / \"kernels\" / \"metatlas-targeted\" / \"kernel.json\"\n",

diff --git a/notebooks/reference/Targeted.ipynb b/notebooks/reference/Targeted.ipynb
@@ -254,7 +254,7 @@
     "\n",
     "parameters = {k: v for k, v in globals().items() if k[0] != \"_\" and k not in [\"In\", \"Out\", \"get_ipython\", \"exit\", \"quit\", \"open\"]}\n",
     "logger = logging.getLogger(\"metatlas.jupyter\")\n",
-    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=doejgi/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
+    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=ghcr.io/biorack/metatlas/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
     "                 \"ipykernel_launcher\",\"-f\",\"{connection_file}\"],\"display_name\": \"Metatlas Targeted\",\"language\": \"python\",\n",
     "                 \"metadata\": { \"debugger\": true }}\"\"\"\n",
     "kernel_file_name = Path.home() / \".local\" / \"share\" / \"jupyter\" / \"kernels\" / \"metatlas-targeted\" / \"kernel.json\"\n",

diff --git a/notebooks/reference/Targeted_hybrid.ipynb b/notebooks/reference/Targeted_hybrid.ipynb
@@ -218,7 +218,7 @@
     "\n",
     "parameters = {k: v for k, v in globals().items() if k[0] != \"_\" and k not in [\"In\", \"Out\", \"get_ipython\", \"exit\", \"quit\", \"open\"]}\n",
     "logger = logging.getLogger(\"metatlas.jupyter\")\n",
-    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=doejgi/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
+    "kernel_def = \"\"\"{\"argv\":[\"shifter\",\"--entrypoint\",\"--image=ghcr.io/biorack/metatlas/metatlas_shifter:latest\",\"/usr/local/bin/python\",\"-m\",\n",
     "                 \"ipykernel_launcher\",\"-f\",\"{connection_file}\"],\"display_name\": \"Metatlas Targeted\",\"language\": \"python\",\n",
     "                 \"metadata\": { \"debugger\": true }}\"\"\"\n",
     "kernel_file_name = Path.home() / \".local\" / \"share\" / \"jupyter\" / \"kernels\" / \"metatlas-targeted\" / \"kernel.json\"\n",

diff --git a/papermill/slurm_template.sh b/papermill/slurm_template.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-#SBATCH --image=docker:doejgi/metatlas_shifter:latest
+#SBATCH --image=docker:ghcr.io/biorack/metatlas/metatlas_shifter:latest
 #SBATCH --nodes=1
 #SBATCH --licenses=cfs
 #SBATCH --mail-type=ALL

diff --git a/utils/raw_to_h5.sh b/utils/raw_to_h5.sh
@@ -57,7 +57,7 @@ if [ -f "$failure_file" ]; then
 fi
 
 function metatlas {
-  shifter "--image=doejgi/metatlas_shifter:latest" \
+  shifter "--image=ghcr.io/biorack/metatlas/metatlas_shifter:latest" \
           "--env=HDF5_USE_FILE_LOCKING=FALSE" \
           "--env=PYTHONPATH=/src" \
 	  "--clearenv" \

diff --git a/utils/validate_config.sh b/utils/validate_config.sh
@@ -4,5 +4,5 @@ set -euo pipefail
 script_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 
 shifter --clearenv --module=none --entrypoint \
-	--image=doejgi/metatlas_shifter:latest \
+	--image=ghcr.io/biorack/metatlas/metatlas_shifter:latest \
 	python "${script_dir}/validate_config.py" "$@"