vitessce · mattscott68 · Sep 29, 2023 · Sep 29, 2023
diff --git a/demos/cosmx_io/Snakefile b/demos/cosmx_io/Snakefile
diff --git a/demos/cosmx_io/config.yml b/demos/cosmx_io/config.yml
@@ -0,0 +1,2 @@
+output:
+- combat_2022_cell.h5ad.zarr
diff --git a/demos/mcmicro_io/Snakefile b/demos/mcmicro_io/Snakefile
diff --git a/demos/merfish/Snakefile b/demos/merfish/Snakefile
diff --git a/demos/mibitof/Snakefile b/demos/mibitof/Snakefile
diff --git a/demos/steinbock_io/Snakefile b/demos/steinbock_io/Snakefile
diff --git a/demos/toy/Snakefile b/demos/toy/Snakefile
@@ -0,0 +1,34 @@
+include: "../common.smk"
+configfile: "config.yml"
+
+# TODO: start from the real raw files
+BASE_URL = "https://s3.embl.de/spatialdata/spatialdata-sandbox/{dataset}.zip"
+
+
+rule all:
+    input:
+        [ (PROCESSED_DIR / f) for f in config['output'] ]
+
+
+# Unzip the downloaded zip files
+rule unzip_file:
+    input:
+        (RAW_DIR / "{dataset}.zip")
+    output:
+        directory(PROCESSED_DIR / "{dataset}.zarr")
+    shell:
+        """
+        unzip {input} -d data/processed &&\
+        mv data/processed/data.zarr data/processed/{wildcards.dataset}.zarr
+        """
+
+# Download visium .zip file containing single-cell data.
+rule download_data:
+    output:
+        (RAW_DIR / "{dataset}.zip")
+    params:
+        file_url=BASE_URL
+    shell:
+        '''
+        curl -L -o {output} {params.file_url}
+        '''
diff --git a/demos/toy/config.yml b/demos/toy/config.yml
@@ -0,0 +1,4 @@
+output:
+- toy.zarr
+- cosmx_io.zarr
+- mcmicro_io.zarr
diff --git a/demos/visium/Snakefile b/demos/visium/Snakefile
diff --git a/demos/visium_associated_xenium_io/Snakefile b/demos/visium_associated_xenium_io/Snakefile
@@ -0,0 +1,34 @@
+include: "../common.smk"
+configfile: "config.yml"
+
+# TODO: start from the real raw files
+BASE_URL = "https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip"
+
+
+rule all:
+    input:
+        [ (PROCESSED_DIR / f) for f in config['output'] ]
+
+
+# Unzip the downloaded zip files
+rule unzip_file:
+    input:
+        os.path.join("data", file_name)
+    output:
+        os.path.join("data", "visium_associated_xenium_io.zip")
+    shell:
+        """
+        mkdir -p {output}\
+        unzip {input} -d {output}\
+        """
+
+# Download visium .zip file containing single-cell data.
+rule download_data:
+    output:
+        (RAW_DIR / "visium_associated_xenium_io.zip")
+    params:
+        file_url=H5AD_URL
+    shell:
+        '''
+        curl -L -o {output} {params.file_url}
+        '''
diff --git a/demos/visium_io/Snakefile b/demos/visium_io/Snakefile
@@ -0,0 +1,34 @@
+include: "../common.smk"
+configfile: "config.yml"
+
+# TODO: start from the real raw files
+BASE_URL = "https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zip"
+
+
+rule all:
+    input:
+        [ (PROCESSED_DIR / f) for f in config['output'] ]
+
+
+# Unzip the downloaded zip files
+rule unzip_file:
+    input:
+        os.path.join("data", file_name)
+    output:
+        os.path.join("data", "visium_io.zip")
+    shell:
+        """
+        mkdir -p {output}\
+        unzip {input} -d {output}\
+        """
+
+# Download visium .zip file containing single-cell data.
+rule download_data:
+    output:
+        (RAW_DIR / "visium_io.zip")
+    params:
+        file_url=H5AD_URL
+    shell:
+        '''
+        curl -L -o {output} {params.file_url}
+        '''
diff --git a/demos/xenium_rep1_io/Snakefile b/demos/xenium_rep1_io/Snakefile
diff --git a/demos/xenium_rep2_io/Snakefile b/demos/xenium_rep2_io/Snakefile