From 1e4b6ce8c77ac9b8ea86aaff96950d32c613fd8b Mon Sep 17 00:00:00 2001 From: Mustafa Tekpinar Date: Wed, 30 Jun 2021 16:56:49 +0200 Subject: [PATCH] Updated installation.rst for dockers updates. --- docs/installation.rst | 55 +++++++++++++++++++++++++++++-------------- 1 file changed, 37 insertions(+), 18 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index c2af85a..7ce9606 100644 --- a/docs/installation.rst +++ b/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. @@ -73,17 +73,20 @@ If you want to install the latest version from the source :: from Docker image ~~~~~~~~~~~~~~~~~ -Docker images are also available from `Docker Hub `_ +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 ``_ 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 @@ -91,19 +94,29 @@ 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 `_ :: - 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