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PRESCOTT
Commit ad6a987f by Mustafa Tekpinar
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Updated the documentation for v1.6.0!

parent dca69ed1
Showing with 210 additions and 104 deletions
Dockerfile
......@@ -98,21 +98,21 @@ RUN pip3 install https://github.com/debbiemarkslab/EVcouplings/archive/develop.z
# If run command on M1 Mac with macOS Monterey, you can remove sudo
# Build command
# sudo docker build -t tekpinar/prescott-docker:v1.5.1 .
# sudo docker build -t tekpinar/prescott-docker:v1.6.0 .
# sudo docker login
# sudo docker push tekpinar/prescott-docker:v1.5.1
# sudo docker push tekpinar/prescott-docker:v1.6.0
# Pull command on M1 Mac with macOS Monterey
# sudo docker pull tekpinar/prescott-docker:v1.5.1
# sudo docker pull tekpinar/prescott-docker:v1.6.0
# Run commands
# sudo docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/prescott-docker:v1.5.1 /bin/bash
# sudo docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/prescott-docker:v1.6.0 /bin/bash
# Bind your current folder to a particular folder in docker.
# In this way, you fall into the bash terminal of the docker image.
# docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.5.1
# docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.6.0
#If you want to use the docker image like an executable file:
# Please note that you must have aliBLAT.fasta and blat-af2.pdb inside your current folder and run this command!
# sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.5.1 escott aliBLAT.fasta --pdbfile blat-af2.pdb
# sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.6.0 escott aliBLAT.fasta --pdbfile blat-af2.pdb
Singularityfile.sh deleted 100644 → 0
#!/bin/bash
#You can not run docker on many high performance computing systems
#due to sudo permissions etc.
#However, singularity can be run on them. Due to this reason, I prepared
#this file to show how you can prepare a singulartiy sif file from docker
#image of PRESCOTT.
#STEP 0: First thing first! You must have singularity installed on your system.
# If not, you can find the installation instructions here:
# https://github.com/sylabs/singularity/blob/main/INSTALL.md
# In addition, there are different releases(deb, rpm or source) in the following page:
# https://github.com/sylabs/singularity/releases
#STEP 1: Building singularity from the docker image online:
# Please note that you will need to change (v1.5.1) to the version you want
# if there is an update in the version.
singularity build prescott-docker-v1.5.1.sif docker://tekpinar/prescott-docker:v1.5.1
#STEP 2: Running escott with the sif file:
singularity exec prescott-docker-v1.5.1.sif escott -h
#STEP 3: Running prescott with the sif file:
singularity exec prescott-docker-v1.5.1.sif prescott -h
#STEP 4: Go to the folder where both aliBLAT.fasta and blat-af2.pdb are located.
# These two files are provided in the data folder of this repository.
# YOUR_SINGULARITY_DIR is where prescott-docker-v1.5.1.sif file located.
singularity exec --home `pwd` $YOUR_SINGULARITY_DIR/prescott-docker-v1.5.1.sif escott aliBLAT.fasta --pdbfile blat-af2.pdb
docs/_build/html/.buildinfo
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 5c84254d67e9b464e3ef5db2238ded56
config: c08592d911c59bb40f4fc837e9874171
tags: 645f666f9bcd5a90fca523b33c5a78b7
docs/_build/html/_sources/index.rst.txt
......@@ -14,6 +14,7 @@ Welcome to PRESCOTT documentation!
docker.rst
analysis.rst
input-preparation.rst
singularity.rst
installation.rst
Indices and tables
......
docs/_build/html/_sources/installation.rst.txt
......@@ -41,7 +41,7 @@ Then, source the saved .profile so that the environment variable will be taken i
JET2 is essential and it should be installed to be able to use PRESCOTT.
Preparation of the environment and installation of PRESCOTT
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step by step installation on Ubuntu 22.04
......
docs/_build/html/_static/documentation_options.js
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.5.0',
VERSION: '1.6.0',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
......
docs/_build/html/analysis.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Analyzing and Modifying the ESCOTT Output &mdash; prescott 1.5.0 documentation</title>
<title>Analyzing and Modifying the ESCOTT Output &mdash; prescott 1.6.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......
docs/_build/html/docker.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Using ESCOTT via Docker &mdash; prescott 1.5.0 documentation</title>
<title>Using ESCOTT via Docker &mdash; prescott 1.6.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......
docs/_build/html/genindex.html
......@@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Index &mdash; prescott 1.5.0 documentation</title>
<title>Index &mdash; prescott 1.6.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -45,6 +45,7 @@
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="singularity.html">Using ESCOTT via Singularity</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul>
......
docs/_build/html/index.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Welcome to PRESCOTT documentation! &mdash; prescott 1.5.0 documentation</title>
<title>Welcome to PRESCOTT documentation! &mdash; prescott 1.6.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -47,6 +47,7 @@
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="singularity.html">Using ESCOTT via Singularity</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul>
......@@ -105,6 +106,7 @@
<li class="toctree-l2"><a class="reference internal" href="input-preparation.html#preparing-your-input-msa-and-pdb-with-colabfold">Preparing Your Input MSA and PDB with Colabfold</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="singularity.html">Using ESCOTT via Singularity</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="installation.html#installing-the-dependencies">Installing the dependencies:</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#preparation-of-the-environment-and-installation-of-prescott">Preparation of the environment and installation of PRESCOTT</a></li>
......
docs/_build/html/input-preparation.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Preparing Your Own Input &mdash; prescott 1.5.0 documentation</title>
<title>Preparing Your Own Input &mdash; prescott 1.6.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......
docs/_build/html/installation.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Installation &mdash; prescott 1.5.0 documentation</title>
<title>Installation &mdash; prescott 1.6.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......@@ -43,8 +43,9 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using PRESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the PRESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#installing-the-dependencies">Installing the dependencies:</a></li>
......
docs/_build/html/introduction.html
......@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Introduction &mdash; prescott 1.5.0 documentation</title>
<title>Introduction &mdash; prescott 1.6.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]>
......
docs/_build/html/search.html
......@@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Search &mdash; prescott 1.5.0 documentation</title>
<title>Search &mdash; prescott 1.6.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
......@@ -48,6 +48,7 @@
<li class="toctree-l1"><a class="reference internal" href="docker.html">Using ESCOTT via Docker</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis.html">Analyzing and Modifying the ESCOTT Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="input-preparation.html">Preparing Your Own Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="singularity.html">Using ESCOTT via Singularity</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul>
......
docs/_build/html/searchindex.js
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docs/_build/latex/prescott.log
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This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex 2023.8.21) 30 NOV 2023 14:59
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......@@ -814,25 +814,29 @@ LaTeX Font Info: Font shape `T1/txtt/m/it' in size <10> not available
Chapter 5.
[13
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Chapter 6.
[15] [16]
Underfull \hbox (badness 7981) in paragraph at lines 904--907
[]\T1/qtm/m/n/10 #Down-load PRESCOTT from [][]$http : / / gitlab . lcqb . upmc
. fr / tekpinar / PRESCOTT$[][] repos-i-tory and go in-side the
[]
[15] [16
[17] [18
]
Chapter 6.
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Chapter 7.
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docs/_build/latex/prescott.tex
......@@ -61,8 +61,8 @@
\title{prescott}
\date{Nov 17, 2023}
\release{1.5.0}
\date{Nov 30, 2023}
\release{1.6.0}
\author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}}
\renewcommand{\releasename}{Release}
......@@ -663,6 +663,81 @@ An input PDB: myprotein.pdb
\sphinxstepscope
\chapter{Using ESCOTT via Singularity}
\label{\detokenize{singularity:using-escott-via-singularity}}\label{\detokenize{singularity::doc}}
\sphinxAtStartPar
You can not run docker on many high performance computing systems
due to sudo permissions etc.
However, singularity can be run on them. Due to this reason, I prepared
this file to show how you can prepare a singulartiy sif file from (online) docker
image of PRESCOTT.
\begin{itemize}
\item {}
\sphinxAtStartPar
STEP 0: First thing first! You must have singularity installed on your system.
\begin{quote}
\sphinxAtStartPar
If not, you can find the installation instructions here:
\sphinxurl{https://github.com/sylabs/singularity/blob/main/INSTALL.md}
\sphinxAtStartPar
In addition, there are different releases(deb, rpm or source) in the following page:
\sphinxurl{https://github.com/sylabs/singularity/releases}
\end{quote}
\item {}
\sphinxAtStartPar
STEP 1: Building singularity from the docker image online:
\begin{quote}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
singularity build prescott\PYGZhy{}docker\PYGZhy{}v1.6.0.sif docker://tekpinar/prescott\PYGZhy{}docker:v1.6.0
\end{sphinxVerbatim}
\sphinxAtStartPar
Please note that you will need to change (v1.6.0) to the version you want if there is an update in the version.
\end{quote}
\item {}
\sphinxAtStartPar
STEP 2: Running escott with the sif file:
\begin{quote}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
singularity \PYG{n+nb}{exec} prescott\PYGZhy{}docker\PYGZhy{}v1.6.0.sif escott \PYGZhy{}h
\end{sphinxVerbatim}
\end{quote}
\item {}
\sphinxAtStartPar
STEP 3: Running prescott with the sif file:
\begin{quote}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
singularity \PYG{n+nb}{exec} prescott\PYGZhy{}docker\PYGZhy{}v1.6.0.sif prescott \PYGZhy{}h
\end{sphinxVerbatim}
\end{quote}
\item {} \begin{description}
\sphinxlineitem{STEP 4: Go to the folder where both aliBLAT.fasta and blat\sphinxhyphen{}af2.pdb are located.}\begin{quote}
\sphinxAtStartPar
These two files are provided in the data folder of this repository.
YOUR\_SINGULARITY\_DIR is where prescott\sphinxhyphen{}docker\sphinxhyphen{}v1.6.0.sif file is located.
\end{quote}
\begin{sphinxVerbatim}[commandchars=\\\{\}]
singularity \PYG{n+nb}{exec} \PYGZhy{}\PYGZhy{}home \PYG{l+s+sb}{`}\PYG{n+nb}{pwd}\PYG{l+s+sb}{`} \PYG{n+nv}{\PYGZdl{}YOUR\PYGZus{}SINGULARITY\PYGZus{}DIR}/prescott\PYGZhy{}docker\PYGZhy{}v1.6.0.sif escott aliBLAT.fasta \PYGZhy{}\PYGZhy{}pdbfile blat\PYGZhy{}af2.pdb
\end{sphinxVerbatim}
\end{description}
\end{itemize}
\sphinxstepscope
\chapter{Installation}
\label{\detokenize{installation:installation}}\label{\detokenize{installation::doc}}
\sphinxAtStartPar
......
docs/_build/latex/prescott.toc
......@@ -23,8 +23,9 @@
\contentsline {section}{\numberline {3.3}Selected Single Point or Multiple Point Mutation Calculations}{10}{section.3.3}%
\contentsline {chapter}{\numberline {4}Preparing Your Own Input}{11}{chapter.4}%
\contentsline {section}{\numberline {4.1}Preparing Your Input MSA and PDB with Colabfold}{11}{section.4.1}%
\contentsline {chapter}{\numberline {5}Installation}{13}{chapter.5}%
\contentsline {section}{\numberline {5.1}Installing the dependencies:}{13}{section.5.1}%
\contentsline {section}{\numberline {5.2}Preparation of the environment and installation of PRESCOTT}{13}{section.5.2}%
\contentsline {section}{\numberline {5.3}Configuring default.conf file}{15}{section.5.3}%
\contentsline {chapter}{\numberline {6}Indices and tables}{17}{chapter.6}%
\contentsline {chapter}{\numberline {5}Using ESCOTT via Singularity}{13}{chapter.5}%
\contentsline {chapter}{\numberline {6}Installation}{15}{chapter.6}%
\contentsline {section}{\numberline {6.1}Installing the dependencies:}{15}{section.6.1}%
\contentsline {section}{\numberline {6.2}Preparation of the environment and installation of PRESCOTT}{15}{section.6.2}%
\contentsline {section}{\numberline {6.3}Configuring default.conf file}{17}{section.6.3}%
\contentsline {chapter}{\numberline {7}Indices and tables}{19}{chapter.7}%
docs/conf.py
......@@ -23,7 +23,7 @@ copyright = '2023, Mustafa Tekpinar'
author = 'Mustafa Tekpinar'
# The full version, including alpha/beta/rc tags
release = '1.5.1'
release = '1.6.0'
# -- General configuration ---------------------------------------------------
......
docs/index.rst
......@@ -14,6 +14,7 @@ Welcome to PRESCOTT documentation!
docker.rst
analysis.rst
input-preparation.rst
singularity.rst
installation.rst
Indices and tables
......
docs/installation.rst
......@@ -41,7 +41,7 @@ Then, source the saved .profile so that the environment variable will be taken i
JET2 is essential and it should be installed to be able to use PRESCOTT.
Preparation of the environment and installation of PRESCOTT
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step by step installation on Ubuntu 22.04
......
docs/singularity.rst 0 → 100644
Using ESCOTT via Singularity
============================
You can not run docker on many high performance computing systems
due to sudo permissions etc.
However, singularity can be run on them. Due to this reason, I prepared
this file to show how you can prepare a singulartiy sif file from (online) docker
image of PRESCOTT.
* STEP 0: First thing first! You must have singularity installed on your system.
If not, you can find the installation instructions here:
https://github.com/sylabs/singularity/blob/main/INSTALL.md
In addition, there are different releases(deb, rpm or source) in the following page:
https://github.com/sylabs/singularity/releases
* STEP 1: Building singularity from the docker image online:
.. code:: bash
singularity build prescott-docker-v1.6.0.sif docker://tekpinar/prescott-docker:v1.6.0
Please note that you will need to change (v1.6.0) to the version you want if there is an update in the version.
* STEP 2: Running escott with the sif file:
.. code:: bash
singularity exec prescott-docker-v1.6.0.sif escott -h
* STEP 3: Running prescott with the sif file:
.. code:: bash
singularity exec prescott-docker-v1.6.0.sif prescott -h
* STEP 4: Go to the folder where both aliBLAT.fasta and blat-af2.pdb are located.
These two files are provided in the data folder of this repository.
YOUR_SINGULARITY_DIR is where prescott-docker-v1.6.0.sif file is located.
.. code:: bash
singularity exec --home `pwd` $YOUR_SINGULARITY_DIR/prescott-docker-v1.6.0.sif escott aliBLAT.fasta --pdbfile blat-af2.pdb
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