Updated installation.rst for dockers updates.

docs/installation.rst

@@ -5,12 +5,6 @@ Basic Installation
 ------------------
 We recommend installing correlationplus with pip or conda for regular users:
 
-with conda
-~~~~~~~~~~
-
-You can also install correlationplus with conda as follows::
-
-    conda install -c bioconda correlationplus
 with pip
 ~~~~~~~~
 We **strongly** encourage you to install correlationplus in a virtualenv::
@@ -36,7 +30,13 @@ you can solve it as follows::
 	python3 -m pip install llvmlite --ignore-installed
 	python3 -m pip install correlationplus
 
-		
+with conda
+~~~~~~~~~~
+
+You can also install correlationplus with conda as follows::
+
+    conda install -c bioconda correlationplus
+    
 Most of the time, at least one these methods will be sufficient for the installation.
 However, if these two methods didn't work for any reason, you can take a look 
 at the 'Advanced Installation' instructions to install it from the source.
@@ -73,37 +73,50 @@ If you want to install the latest version from the source ::
 from Docker image
 ~~~~~~~~~~~~~~~~~
 
-Docker images are also available from `Docker Hub <https://hub.docker.com/r/structuraldynamicslab/correlationplus>`_
+If you don't want to install or can't install correlatioplus for any reason, you can use docker images. These images do not require any installation. 
+You can find docker images for correlationplus  at `<https://hub.docker.com/r/structuraldynamicslab/correlationplus>`_
 
 The computation inside the container will be performed under **correlationplus** id in **/home/correlationplus** directory.
 So before running a **correlationplus** container,
 do not forget to create and mount a shared directory in the container. 
 
-This directory must be writable to this user. So you have two possibilities
+This directory must be writable to this user. So, you have two possibilities:
+
+1. Map your id on the host to the *correlationplus* user in the container::
 
-    1. map your id on the host to the *correlationplus* user in the container
        ``-u $(id -u ${USER}):$(id -g ${USER})``
-    2. make the shared directory writable to anyone
+2. Make the shared directory writable to anyone::
+
        ``chmod 777 shared_dir``
 
 option 1
 
 .. code-block:: shell
 
     mkdir shared_dir
-    cp 6fl9_just_prot_anm_100_modes_rc_15_cross-correlations.txt 6fl9_centeredOrientedAligned2Z.pdb shared_dir
+    cp 6lu7_dimer_no_ligand_protein_sim1-lmi.dat shared_dir
+    cp 6lu7_dimer_with_N3_protein_sim1-lmi.dat shared_dir
+    cp 6lu7_dimer_with_N3_protein_sim1_ca.pdb shared_dir
     cd shared_dir
-    docker run -v $PWD:/home/correlationplus -u $(id -u ${USER}):$(id -g ${USER}) structuraldynamicslab/correlation_plus diffMap -i 6fl9_rc15_scalCoeff1_100_modes_lmi_v2.dat -j zacharias_rc15_scalCoeff15_100_modes_lmi.dat -p 6fl9_centeredOrientedAligned2Z.pdb -t lmi
+    docker run -v $PWD:/home/correlationplus -u $(id -u ${USER}):$(id -g ${USER}) structuraldynamicslab/correlation_plus diffMap\
+    				-i 6lu7_dimer_no_ligand_protein_sim1-lmi.dat \
+				-j 6lu7_dimer_with_N3_protein_sim1-lmi.dat \
+				-p 6lu7_dimer_with_N3_protein_sim1_ca.pdb -t lmi
 
 option 2
 
 .. code-block:: shell
 
     mkdir shared_dir
-    cp 6fl9_just_prot_anm_100_modes_rc_15_cross-correlations.txt 6fl9_centeredOrientedAligned2Z.pdb shared_dir
+    cp 6lu7_dimer_no_ligand_protein_sim1-lmi.dat shared_dir
+    cp 6lu7_dimer_with_N3_protein_sim1-lmi.dat shared_dir
+    cp 6lu7_dimer_with_N3_protein_sim1_ca.pdb shared_dir
     chmod 777 shared_dir
     cd shared_dir
-    docker run -v $PWD:/home/correlationplus structuraldynamicslab/correlation_plus diffMap -i 6fl9_rc15_scalCoeff1_100_modes_lmi_v2.dat -j zacharias_rc15_scalCoeff15_100_modes_lmi.dat -p 6fl9_centeredOrientedAligned2Z.pdb -t lmi
+    docker run -v $PWD:/home/correlationplus structuraldynamicslab/correlation_plus diffMap \
+    						-i 6lu7_dimer_no_ligand_protein_sim1-lmi.dat \
+						-j 6lu7_dimer_with_N3_protein_sim1-lmi.dat \
+						-p 6lu7_dimer_with_N3_protein_sim1-lmi.dat -t lmi
 
 
 It is also possible to run an ipython interactive session::
@@ -119,14 +132,20 @@ from Singularity image
 
 As the docker image is registered in dockerhub you can also use it directly with `Singularity <https://sylabs.io/docs/>`_ ::
 
-    singularity run docker://structuraldynamicslab/correlationplus diffMap -i 6fl9_rc15_scalCoeff1_100_modes_lmi_v2.dat -j zacharias_rc15_scalCoeff15_100_modes_lmi.dat -p 6fl9_centeredOrientedAligned2Z.pdb -t lmi
+    singularity run docker://structuraldynamicslab/correlationplus diffMap \
+    					-i 6lu7_dimer_no_ligand_protein_sim1-lmi.dat \
+					-j 6lu7_dimer_with_N3_protein_sim1-lmi.dat \
+					-p 6lu7_dimer_with_N3_protein_sim1_ca.pdb -t lmi
 
 or in 2 steps ::
 
     singularity pull correlationplus.simg docker://structuraldynamicslab/correlation_plus
-    ./correlationplus.simg diffMap -i 6fl9_rc15_scalCoeff1_100_modes_lmi_v2.dat -j zacharias_rc15_scalCoeff15_100_modes_lmi.dat -p 6fl9_centeredOrientedAligned2Z.pdb -t lmi
+    ./correlationplus.simg diffMap \
+    			-i 6lu7_dimer_no_ligand_protein_sim1-lmi.dat \
+			-j 6lu7_dimer_with_N3_protein_sim1-lmi.dat \
+			-p 6lu7_dimer_with_N3_protein_sim1_ca.pdb -t lmi
 
-Unlike docker you do not have to worry about shared directory, your *home* and */tmp* are automatically shared.
+Unlike docker, you do not have to worry about shared directory, your *home* and */tmp* are automatically shared.
 You can also run an *ipython* interactive session ::
 
     singularity shell correlationplus.simg