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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 ...@@ -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 # If run command on M1 Mac with macOS Monterey, you can remove sudo
# Build command # 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 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 # 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 # 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 $(pwd) --platform linux/amd64 tekpinar/prescott-docker:v1.6.0 /bin/bash
# Bind your current folder to a particular folder in docker. # Bind your current folder to a particular folder in docker.
# In this way, you fall into the bash terminal of the docker image. # In this way, you fall into the bash terminal of the docker image.
# docker run -ti --rm --mount type=bind,source=$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: #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! # 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 # 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. # 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 tags: 645f666f9bcd5a90fca523b33c5a78b7
docs/_build/html/_sources/index.rst.txt
...@@ -14,6 +14,7 @@ Welcome to PRESCOTT documentation! ...@@ -14,6 +14,7 @@ Welcome to PRESCOTT documentation!
docker.rst docker.rst
analysis.rst analysis.rst
input-preparation.rst input-preparation.rst
singularity.rst
installation.rst installation.rst
Indices and tables 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 ...@@ -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. JET2 is essential and it should be installed to be able to use PRESCOTT.
Preparation of the environment and installation of PRESCOTT Preparation of the environment and installation of PRESCOTT
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step by step installation on Ubuntu 22.04 Step by step installation on Ubuntu 22.04
......
docs/_build/html/_static/documentation_options.js
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '1.5.0', VERSION: '1.6.0',
LANGUAGE: 'en', LANGUAGE: 'en',
COLLAPSE_INDEX: false, COLLAPSE_INDEX: false,
BUILDER: 'html', BUILDER: 'html',
......
docs/_build/html/analysis.html
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" /> <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" /> <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/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]> <!--[if lt IE 9]>
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docs/_build/html/docker.html
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" /> <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" /> <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/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]> <!--[if lt IE 9]>
......
docs/_build/html/genindex.html
...@@ -3,7 +3,7 @@ ...@@ -3,7 +3,7 @@
<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /> <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/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]> <!--[if lt IE 9]>
...@@ -45,6 +45,7 @@ ...@@ -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="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="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="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> <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul> </ul>
......
docs/_build/html/index.html
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" /> <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" /> <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/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]> <!--[if lt IE 9]>
...@@ -47,6 +47,7 @@ ...@@ -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="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="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="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> <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul> </ul>
...@@ -105,6 +106,7 @@ ...@@ -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> <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> </ul>
</li> </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-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#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> <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 @@ ...@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" /> <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" /> <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/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]> <!--[if lt IE 9]>
......
docs/_build/html/installation.html
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" /> <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" /> <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/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]> <!--[if lt IE 9]>
...@@ -43,8 +43,9 @@ ...@@ -43,8 +43,9 @@
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu"> </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> <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul class="current"> <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="introduction.html">Introduction</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="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="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-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> <li class="toctree-l2"><a class="reference internal" href="#installing-the-dependencies">Installing the dependencies:</a></li>
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docs/_build/html/introduction.html
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" /> <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" /> <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/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<!--[if lt IE 9]> <!--[if lt IE 9]>
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docs/_build/html/search.html
...@@ -3,7 +3,7 @@ ...@@ -3,7 +3,7 @@
<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /> <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/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" /> <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
...@@ -48,6 +48,7 @@ ...@@ -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="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="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="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> <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
</ul> </ul>
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docs/_build/html/searchindex.js
Search.setIndex({"docnames": ["analysis", "docker", "index", "input-preparation", "installation", "introduction"], "filenames": ["analysis.rst", "docker.rst", "index.rst", "input-preparation.rst", "installation.rst", "introduction.rst"], "titles": ["Analyzing and Modifying the ESCOTT Output", "Using ESCOTT via Docker", "Welcome to PRESCOTT documentation!", "Preparing Your Own Input", "Installation", "Introduction"], "terms": {"There": [0, 3], "hardcod": 0, "limit": 0, "howev": [0, 1, 3, 5], "valu": 0, "rang": 0, "between": 0, "12": 0, "2": [0, 5], "gener": 0, "The": [0, 1, 3, 5], "lower": 0, "mean": 0, "impact": [0, 1, 3], "while": 0, "close": 0, "0": [0, 1, 3, 4, 5], "doe": [0, 3], "have": [0, 1, 3, 4, 5], "ani": [0, 5], "signific": 0, "we": [0, 1, 3, 4, 5], "should": [0, 4, 5], "note": [0, 1, 4, 5], "most": [0, 5], "ar": [0, 1, 3, 4, 5], "deleteri": 0, "alwai": 0, "case": [0, 1, 4], "By": [0, 5], "default": [0, 2, 5], "onli": [0, 1, 4, 5], "combin": [0, 5], "independ": 0, "epistat": 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Chapter 5. Chapter 5.
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Chapter 6.
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[]\T1/qtm/m/n/10 #Down-load PRESCOTT from [][]$http : / / gitlab . lcqb . upmc []\T1/qtm/m/n/10 #Down-load PRESCOTT from [][]$http : / / gitlab . lcqb . upmc
. fr / tekpinar / PRESCOTT$[][] repos-i-tory and go in-side the . fr / tekpinar / PRESCOTT$[][] repos-i-tory and go in-side the
[] []
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] ]
Chapter 6. Chapter 7.
(./prescott.ind) [17] (./prescott.aux) (./prescott.ind) [19] (./prescott.aux)
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docs/_build/latex/prescott.out
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docs/_build/latex/prescott.tex
...@@ -61,8 +61,8 @@ ...@@ -61,8 +61,8 @@
\title{prescott} \title{prescott}
\date{Nov 17, 2023} \date{Nov 30, 2023}
\release{1.5.0} \release{1.6.0}
\author{Mustafa Tekpinar} \author{Mustafa Tekpinar}
\newcommand{\sphinxlogo}{\vbox{}} \newcommand{\sphinxlogo}{\vbox{}}
\renewcommand{\releasename}{Release} \renewcommand{\releasename}{Release}
...@@ -663,6 +663,81 @@ An input PDB: myprotein.pdb ...@@ -663,6 +663,81 @@ An input PDB: myprotein.pdb
\sphinxstepscope \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} \chapter{Installation}
\label{\detokenize{installation:installation}}\label{\detokenize{installation::doc}} \label{\detokenize{installation:installation}}\label{\detokenize{installation::doc}}
\sphinxAtStartPar \sphinxAtStartPar
......
docs/_build/latex/prescott.toc
...@@ -23,8 +23,9 @@ ...@@ -23,8 +23,9 @@
\contentsline {section}{\numberline {3.3}Selected Single Point or Multiple Point Mutation Calculations}{10}{section.3.3}% \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 {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 {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 {chapter}{\numberline {5}Using ESCOTT via Singularity}{13}{chapter.5}%
\contentsline {section}{\numberline {5.1}Installing the dependencies:}{13}{section.5.1}% \contentsline {chapter}{\numberline {6}Installation}{15}{chapter.6}%
\contentsline {section}{\numberline {5.2}Preparation of the environment and installation of PRESCOTT}{13}{section.5.2}% \contentsline {section}{\numberline {6.1}Installing the dependencies:}{15}{section.6.1}%
\contentsline {section}{\numberline {5.3}Configuring default.conf file}{15}{section.5.3}% \contentsline {section}{\numberline {6.2}Preparation of the environment and installation of PRESCOTT}{15}{section.6.2}%
\contentsline {chapter}{\numberline {6}Indices and tables}{17}{chapter.6}% \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' ...@@ -23,7 +23,7 @@ copyright = '2023, Mustafa Tekpinar'
author = 'Mustafa Tekpinar' author = 'Mustafa Tekpinar'
# The full version, including alpha/beta/rc tags # The full version, including alpha/beta/rc tags
release = '1.5.1' release = '1.6.0'
# -- General configuration --------------------------------------------------- # -- General configuration ---------------------------------------------------
......
docs/index.rst
...@@ -14,6 +14,7 @@ Welcome to PRESCOTT documentation! ...@@ -14,6 +14,7 @@ Welcome to PRESCOTT documentation!
docker.rst docker.rst
analysis.rst analysis.rst
input-preparation.rst input-preparation.rst
singularity.rst
installation.rst installation.rst
Indices and tables Indices and tables
......
docs/installation.rst
...@@ -41,7 +41,7 @@ Then, source the saved .profile so that the environment variable will be taken i ...@@ -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. JET2 is essential and it should be installed to be able to use PRESCOTT.
Preparation of the environment and installation of PRESCOTT Preparation of the environment and installation of PRESCOTT
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step by step installation on Ubuntu 22.04 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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