diff --git a/singularity/Singularity.1.7.1 b/singularity/Singularity.1.7.1
index 9cbfc4a6e905d162c4a7979bc9435e563c4021d4..b3c30c75cb861e775a822d36c69342b52bc0bf50 100644
--- a/singularity/Singularity.1.7.1
+++ b/singularity/Singularity.1.7.1
@@ -200,6 +200,7 @@ EOF
jupyter nbextension enable nglview --py --sys-prefix
# GO HOME AND CLEANUP
+#####################
apt-get purge -y cmake \
wget \
git \
@@ -212,7 +213,6 @@ apt-get clean
apt-get autoremove -y
cd $SRC_FOLDER && rm -rf $SRC_FOLDER/*
-#########
cd /home
@@ -221,6 +221,7 @@ cd /home
# ENVIRONMENT
##############################################################################
export OST_ROOT="/usr/local"
+export OPENSTRUCTURE_VERSION="1.7.1"
export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64"
export QT_X11_NO_MITSHM=1
@@ -242,18 +243,85 @@ $OST_ROOT/bin/chemdict_tool "$@"
##############################################################################
$OST_ROOT/bin/lddt "$@"
+%apphelp lDDT
+The Local Distance Difference Test.
+
+Usage:
+
+ singularity run --app lDDT <IMAGE> [options] <mod1> [mod1 [mod2]] <re1>[,ref2,ref3]
+
+Options:
+ -s selection performed on ref
+ -c use Calphas only
+ -f perform structural checks and filter input data
+ -t fault tolerant parsing
+ -p <file> use specified parmeter file. Mandatory
+ -v <level> verbosity level (0=results only,1=problems reported, 2=full report)
+ -b <value> tolerance in stddevs for bonds
+ -a <value> tolerance in stddevs for angles
+ -r <value> distance inclusion radius
+ -i <value> sequence separation
+ -e print version
+ -x ignore residue name consistency checks
+
%apprun Molck
##############################################################################
# MOLCK APP
##############################################################################
$OST_ROOT/bin/molck "$@"
+%apphelp Molck
+This is molck - the molecule checker
+
+Usage:
+ singularity run --app Molck <IMAGE> [options] file1.pdb [file2.pdb [...]]
+
+Options:
+ --complib=path location of the compound library file. If not provided, the
+ following locations are searched in this order:
+ 1. Working directory, 2. OpenStructure standard library location (if the
+ executable is part of a standard OpenStructure installation)
+ --rm=<a>,<b> remove atoms and residues matching some criteria
+ zeroocc - Remove atoms with zero occupancy
+ hyd - Remove hydrogen atoms
+ oxt - Remove terminal oxygens
+ nonstd - Remove all residues not one of the 20 standard amino acids
+ unk - Remove unknown and atoms not following the nomenclature
+ --fix-ele clean up element column
+ --stdout write cleaned file(s) to stdout
+ --out=filename write cleaned file(s) to disk. % characters in the filename are
+ replaced with the basename of the input file without extension.
+ Default: %-molcked.pdb
+ --color=auto|on|off
+ whether output should be colored
+ --map-nonstd maps modified residues back to the parent amino acid, for example
+ MSE -> MET, SEP -> SER.
+
%apprun OST
##############################################################################
# OST APP
##############################################################################
$OST_ROOT/bin/ost "$@"
+%apphelp OST
+The OST app exposes OpenStructure binary and can be used to run interactive shell
+and scripts.
+
+Usage:
+ singularity run --app OST <IMAGE> [ost options] [script to execute] [script parameters]
+
+Options:
+ -i, --interactive start interpreter interactively (must be first
+ parameter, ignored otherwise)
+ -h, --help show this help message and exit
+ -v VLEVEL, --verbosity_level=VLEVEL
+ sets the verbosity level [default: 2]
+
+If script requires some external files eg. PDBs, they have to be located in the
+path accessible via mounted volumes. By default Singularity mounts $HOME and
+goes to CWD. Thus this sould work as expected out of the box.
+
+
%appenv IPython
##############################################################################
# NOTEBOOK ENV
@@ -267,6 +335,17 @@ export DNG_INITDIR=${DNG_ROOT}/lib64/python2.7/site-packages/ost
##############################################################################
. $VIRTUALENV_DIR/bin/activate && ipython -i $DNG_INITDIR/ost_startup.py "$@"
+%apphelp IPython
+OST-powered iPython shell.
+
+Usage:
+
+ singularity run --app IPython <IMAGE> [options]
+
+Detailed help:
+
+ singularity run --app IPython <IMAGE> --help
+
%appenv Notebook
##############################################################################
# NOTEBOOK ENV
@@ -281,6 +360,29 @@ export XDG_RUNTIME_DIR=""
##############################################################################
. $VIRTUALENV_DIR/bin/activate && jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@"
+%apphelp Notebook
+A Jupyter notebook palyground with OST and nglview.
+
+Usage:
+
+ singularity run --app Notebook <IMAGE> [options]
+
+The Jupyter notebook is run by default with `--NotebookApp.iopub_data_rate_limit=10000000`
+and `--no-browser` options.
+
+Useful options when running on remote server:
+ --ip=<Unicode> (NotebookApp.ip)
+ Default: 'localhost'
+ The IP address the notebook server will listen on.
+ --port=<Integer> (NotebookApp.port)
+ Default: 8888
+ The port the notebook server will listen on.
+
+To list of all available options:
+
+ singularity run --app Notebook <IMAGE> --help
+
+
%runscript
##############################################################################
# RUNSCRIPT
@@ -294,12 +396,26 @@ This container includes the following apps:
* Notebook - A Jupyter notebook palyground with OST and nglview
* lDDT - The Local Distance Difference Test
* Molck - Molecular checker
+ * ChemdictTool - Creating or update a compound library
To see the help for each individual app run:
- $ singularity run --app APP <IMAGE NAME>
+ singularity help --app <APP NAME> <IMAGE NAME>
+EOF
+%help
+Singularity container for OST $OPENSTRUCTURE_VERSION.
-EOF
+This container includes the following apps:
+ * OST - OpenStructure binary
+ * IPython - OST-powered iPython shell
+ * Notebook - A Jupyter notebook palyground with OST and nglview
+ * lDDT - The Local Distance Difference Test
+ * Molck - Molecular checker
+ * ChemdictTool - Creating or update a compound library
+
+To see the help for each individual app run:
+
+ singularity help --app <APP NAME> <IMAGE NAME>