diff --git a/doc/container/docker.rst b/doc/container/docker.rst index 792890b6aeed2333e9bcc5176d36a172fe30f0a6..808ed9c1ac447895a33cbb241407547e21759b51 100644 --- a/doc/container/docker.rst +++ b/doc/container/docker.rst @@ -113,7 +113,7 @@ To run a script with the upated compound library, use the -v option for mounting .. code-block:: bash 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 with COMPLIB_DIR_LOCALHOST being the directory that contains the newly generated diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst index 6b614edce4d9865430998497244469104ca91127..85b7a525b04c252d4c43059a8d31c9efce17e6ec 100644 --- a/doc/container/singularity.rst +++ b/doc/container/singularity.rst @@ -43,13 +43,13 @@ To see the help for each individual app run: .. code-block:: bash - singularity help --app <APP NAME> <PATH TO PROMOD IMAGE> + singularity run-help --app <APP NAME> <PATH TO PROMOD IMAGE> Eg.: .. code-block:: bash - singularity help --app PM promod.img + singularity run-help --app PM promod.img To list all available ProMod3 modelling actions: @@ -74,14 +74,15 @@ Build a new library: .. code-block:: bash singularity run --app ChemdictTool <IMAGE> create components.cif.gz \ - compounds.chemlib + compounds.chemlib Run some script with an updated compound library from localhost: .. code-block:: bash - singularity run -B <COMPLIB_DIR_LOCALHOST>:<COMPLIB_DIR_CONTAINER> --app PM \ - <IMAGE> my_script.py + singularity run \ + -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, <COMPLIB_DIR_CONTAINER> should be /usr/local/share/openstructure.