diff --git a/biobb_gromacs/docs/source/command_line.md b/biobb_gromacs/docs/source/command_line.md index 867ba35..a69bc2c 100644 --- 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 index eefdefd..f147117 100644 --- 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 index d85c21e..2162037 100644 --- 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 index a92c731..2def855 100644 --- 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 index b4c8e99..0e4a3d4 100644 --- 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 index fdd10df..135edcc 100644 --- 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 index c3ce8bf..617902e 100644 --- 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 index 8682f01..23788a2 100644 --- 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 index 3322ef2..50acfcf 100644 --- 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 index 9c6d82c..a7e0342 100644 --- 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 index bb5f003..1ce505f 100644 --- 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 index 7953fe5..d8747b8 100644 --- 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 index 04a1e02..9d2fcef 100644 --- 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,