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Commit 7b0de369 authored by Bienchen's avatar Bienchen
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SCHWED-4667: Update documentation

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...@@ -113,7 +113,7 @@ To run a script with the upated compound library, use the -v option for mounting ...@@ -113,7 +113,7 @@ To run a script with the upated compound library, use the -v option for mounting
.. code-block:: bash .. code-block:: bash
docker run --rm -v /home/<USER>:/home \ docker run --rm -v /home/<USER>:/home \
-v <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> \ -v <COMPLIB_DIR_LOCALHOST>/compounds.chemlib:<COMPLIB_DIR_CONTAINER>/compounds.chemlib \
<IMAGE_NAME> script.py pdbs/struct.pdb <IMAGE_NAME> script.py pdbs/struct.pdb
with COMPLIB_DIR_LOCALHOST being the directory that contains the newly generated with COMPLIB_DIR_LOCALHOST being the directory that contains the newly generated
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...@@ -43,13 +43,13 @@ To see the help for each individual app run: ...@@ -43,13 +43,13 @@ To see the help for each individual app run:
.. code-block:: bash .. code-block:: bash
singularity help --app <APP NAME> <PATH TO PROMOD IMAGE> singularity run-help --app <APP NAME> <PATH TO PROMOD IMAGE>
Eg.: Eg.:
.. code-block:: bash .. code-block:: bash
singularity help --app PM promod.img singularity run-help --app PM promod.img
To list all available ProMod3 modelling actions: To list all available ProMod3 modelling actions:
...@@ -74,14 +74,15 @@ Build a new library: ...@@ -74,14 +74,15 @@ Build a new library:
.. code-block:: bash .. code-block:: bash
singularity run --app ChemdictTool <IMAGE> create components.cif.gz \ singularity run --app ChemdictTool <IMAGE> create components.cif.gz \
compounds.chemlib compounds.chemlib
Run some script with an updated compound library from localhost: Run some script with an updated compound library from localhost:
.. code-block:: bash .. code-block:: bash
singularity run -B <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> --app PM \ singularity run \
<IMAGE> my_script.py -B <COMPLIB_DIR_LOCALHOST>/compounds.chemlib:<COMPLIB_DIR_CONTAINER>/compounds.chemlib \
--app PM <IMAGE> my_script.py
Same as for the Docker, if you didn't meddle with the original Dockerfile, Same as for the Docker, if you didn't meddle with the original Dockerfile,
<COMPLIB_DIR_CONTAINER> should be /usr/local/share/openstructure. <COMPLIB_DIR_CONTAINER> should be /usr/local/share/openstructure.
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