cellarr 0.4.1.dev2__tar.gz → 0.5.0__tar.gz

{cellarr-0.4.1.dev2 → cellarr-0.5.0}/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.5.0
+
+- Construct cellarr TileDB files on HPC environments based on slurm
+(reference: [#61](https://github.com/BiocPy/cellarr/pull/61))
+
 ## Version 0.4.0
 
 - chore: Remove Python 3.8 (EOL).

{cellarr-0.4.1.dev2 → cellarr-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellarr
-Version: 0.4.1.dev2
+Version: 0.5.0
 Summary: TileDB-based array storage for genomics data collections.
 Home-page: https://github.com/BiocPy/cellarr
 Author: Jayaram Kancherla
@@ -166,7 +166,8 @@ A minimal manifest file (json) must contain the following fields
 - `"python_env"`: A set of commands to activate the Python environment containing this package and its dependencies.
 
 Here’s an example of the manifest file:
-```json
+
+```py
 manifest = {
     "files": your/list/of/files,
     "python_env": """
@@ -187,14 +188,18 @@ which python
         }
     ],
 }
+
+import json
+json.dump(manifest, open("your/path/to/manifest.json", "w"))
 ```
+
 For more options, check out the [README](./src/cellarr/slurm/README.md).
 
 - Step 2: Submit the job
 Once your manifest file is ready, you can submit the necessary jobs using the `cellarr_build` CLI. Run the following command:
 
 ```sh
-cellarr_build --input-manifest your/path/to/test_manifest.json --output-dir your/path/to/output --memory-per-job 8 --cpus-per-task 2
+cellarr_build --input-manifest your/path/to/manifest.json --output-dir your/path/to/output --memory-per-job 8 --cpus-per-task 2
 ```
 
 ### Query a `CellArrDataset`

{cellarr-0.4.1.dev2 → cellarr-0.5.0}/README.md

@@ -133,7 +133,8 @@ A minimal manifest file (json) must contain the following fields
 - `"python_env"`: A set of commands to activate the Python environment containing this package and its dependencies.
 
 Here’s an example of the manifest file:
-```json
+
+```py
 manifest = {
     "files": your/list/of/files,
     "python_env": """
@@ -154,14 +155,18 @@ which python
         }
     ],
 }
+
+import json
+json.dump(manifest, open("your/path/to/manifest.json", "w"))
 ```
+
 For more options, check out the [README](./src/cellarr/slurm/README.md).
 
 - Step 2: Submit the job
 Once your manifest file is ready, you can submit the necessary jobs using the `cellarr_build` CLI. Run the following command:
 
 ```sh
-cellarr_build --input-manifest your/path/to/test_manifest.json --output-dir your/path/to/output --memory-per-job 8 --cpus-per-task 2
+cellarr_build --input-manifest your/path/to/manifest.json --output-dir your/path/to/output --memory-per-job 8 --cpus-per-task 2
 ```
 
 ### Query a `CellArrDataset`

{cellarr-0.4.1.dev2 → cellarr-0.5.0}/src/cellarr.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellarr
-Version: 0.4.1.dev2
+Version: 0.5.0
 Summary: TileDB-based array storage for genomics data collections.
 Home-page: https://github.com/BiocPy/cellarr
 Author: Jayaram Kancherla
@@ -166,7 +166,8 @@ A minimal manifest file (json) must contain the following fields
 - `"python_env"`: A set of commands to activate the Python environment containing this package and its dependencies.
 
 Here’s an example of the manifest file:
-```json
+
+```py
 manifest = {
     "files": your/list/of/files,
     "python_env": """
@@ -187,14 +188,18 @@ which python
         }
     ],
 }
+
+import json
+json.dump(manifest, open("your/path/to/manifest.json", "w"))
 ```
+
 For more options, check out the [README](./src/cellarr/slurm/README.md).
 
 - Step 2: Submit the job
 Once your manifest file is ready, you can submit the necessary jobs using the `cellarr_build` CLI. Run the following command:
 
 ```sh
-cellarr_build --input-manifest your/path/to/test_manifest.json --output-dir your/path/to/output --memory-per-job 8 --cpus-per-task 2
+cellarr_build --input-manifest your/path/to/manifest.json --output-dir your/path/to/output --memory-per-job 8 --cpus-per-task 2
 ```
 
 ### Query a `CellArrDataset`