[UPDATE] Adding sandbox_path property to the json schemas

bioexcel · Jul 4, 2024 · 918b6c5 · 918b6c5
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diff --git a/biobb_gromacs/docs/source/command_line.md b/biobb_gromacs/docs/source/command_line.md
@@ -64,6 +64,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (None) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -169,6 +170,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -277,6 +279,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (None) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -449,6 +452,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -574,6 +578,7 @@ Config parameters for this building block:
 * **gmx_lib** (*string*): (None) Path set GROMACS GMXLIB environment variable..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -688,6 +693,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -766,7 +772,20 @@ Command:
 ```python
 append_ligand -h
 ```
-    /bin/sh: /Users/pau/mambaforge/envs/dev38/bin/append_ligand: Permission denied
+    usage: append_ligand [-h] [-c CONFIG] --input_top_zip_path INPUT_TOP_ZIP_PATH --input_itp_path INPUT_ITP_PATH --output_top_zip_path OUTPUT_TOP_ZIP_PATH [--input_posres_itp_path INPUT_POSRES_ITP_PATH]
+
+    Wrapper of the GROMACS editconf module.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -c CONFIG, --config CONFIG
+                            This file can be a YAML file, JSON file or JSON string
+      --input_posres_itp_path INPUT_POSRES_ITP_PATH
+
+    required arguments:
+      --input_top_zip_path INPUT_TOP_ZIP_PATH
+      --input_itp_path INPUT_ITP_PATH
+      --output_top_zip_path OUTPUT_TOP_ZIP_PATH
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
@@ -782,6 +801,7 @@ Config parameters for this building block:
 * **posres_name** (*string*): (POSRES_LIGAND) String to be included in the ifdef clause..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_gromacs/blob/master/biobb_gromacs/test/data/config/config_append_ligand.yml)
 ```python
@@ -847,6 +867,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -959,6 +980,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -1066,6 +1088,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (None) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -1211,6 +1234,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..
@@ -1356,6 +1380,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (gmx) Path to the GROMACS executable binary..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 * **container_path** (*string*): (None) Path to the binary executable of your container..
 * **container_image** (*string*): (gromacs/gromacs:latest) Container Image identifier..
 * **container_volume_path** (*string*): (/data) Path to an internal directory in the container..

diff --git a/biobb_gromacs/json_schemas/append_ligand.json b/biobb_gromacs/json_schemas/append_ligand.json
@@ -105,6 +105,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_gromacs/json_schemas/editconf.json b/biobb_gromacs/json_schemas/editconf.json
@@ -143,6 +143,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/genion.json b/biobb_gromacs/json_schemas/genion.json
@@ -157,6 +157,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/genrestr.json b/biobb_gromacs/json_schemas/genrestr.json
@@ -120,6 +120,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/gmxselect.json b/biobb_gromacs/json_schemas/gmxselect.json
@@ -120,6 +120,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/grompp.json b/biobb_gromacs/json_schemas/grompp.json
@@ -200,6 +200,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/grompp_mdrun.json b/biobb_gromacs/json_schemas/grompp_mdrun.json
@@ -368,6 +368,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/make_ndx.json b/biobb_gromacs/json_schemas/make_ndx.json
@@ -114,6 +114,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/mdrun.json b/biobb_gromacs/json_schemas/mdrun.json
@@ -279,6 +279,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/pdb2gmx.json b/biobb_gromacs/json_schemas/pdb2gmx.json
@@ -245,6 +245,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/solvate.json b/biobb_gromacs/json_schemas/solvate.json
@@ -151,6 +151,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,

diff --git a/biobb_gromacs/json_schemas/trjcat.json b/biobb_gromacs/json_schemas/trjcat.json
@@ -110,6 +110,12 @@
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
                 },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
+                },
                 "container_path": {
                     "type": "string",
                     "default": null,