Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
P
ProMod3
Manage
Activity
Members
Plan
Jira
Code
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Deploy
Releases
Container registry
Model registry
Analyze
Contributor analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
schwede
ProMod3
Commits
7b0de369
Commit
7b0de369
authored
5 years ago
by
Bienchen
Browse files
Options
Downloads
Patches
Plain Diff
SCHWED-4667
: Update documentation
parent
ea3b82de
No related branches found
No related tags found
No related merge requests found
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
doc/container/docker.rst
+1
-1
1 addition, 1 deletion
doc/container/docker.rst
doc/container/singularity.rst
+6
-5
6 additions, 5 deletions
doc/container/singularity.rst
with
7 additions
and
6 deletions
doc/container/docker.rst
+
1
−
1
View file @
7b0de369
...
@@ -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
...
...
This diff is collapsed.
Click to expand it.
doc/container/singularity.rst
+
6
−
5
View file @
7b0de369
...
@@ -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.
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment