Documentación apps bwa,bamtools,htslib,samtools

docs/source/software/applications/BWA/bwa-0.7.17/index.rst

@@ -17,8 +17,7 @@ Dependencies
 ------------
 
 - gcc-11.2.0
-- samtools
-- htslib
+
 
 Installation
 ------------

docs/source/software/applications/SAMtools/index.rst

@@ -1,22 +1,20 @@
-.. _SAMtools:
+.. _samtools-index:
 
-********
-SAMtools
-********
+SAMTOOLS
+=====
 
-Description
------------
+[1] Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
 
-BWA is a software package for mapping low-divergent sequences against a large reference genome, 
-such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. 
-The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for 
-longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as 
-long-read support and split alignment, but BWA-MEM, which is the latest, is generally 
-recommended for high-quality queries as it is faster and more accurate. 
-BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.s. 
+- Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
+- BCFtools: Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
+- HTSlib: A C library for reading/writing high-throughput sequencing data
 
+Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.
 .. toctree::
-    :caption: Versions
-    :maxdepth: 1
+   :caption: Versions
+   :maxdepth: 1
 
-    SAMtools-1.3.1/index
+   samtools-1.20.0/index
+
+.. [1] SamTools. (s. f.). https://www.htslib.org/
+       Retrieved 8:13, June 17, 2023

docs/source/software/applications/SAMtools/samtools-1.20.0/index.rst

@@ -0,0 +1,116 @@
+.. _samtools-1.20.0-index:
+
+.. role:: bash(code)
+   :language: bash
+
+Samtools 1.20.0
+==============
+
+.. contents:: Table of Contents
+
+Basic information
+------------------
+
+- **Installation Date:** 17/06/2024
+- **Official Website:** https://github.com/samtools/samtools
+- **Installed on:** :ref:`Apolo II <about_apolo-ii>`
+- **License:** GPL
+
+Dependencies
+------------
+
+- gcc-11.2.0
+- htslib
+
+
+Tested on (Requirements)
+------------------------
+
+* **OS base:** CentOS (x86_64) :math:`\boldsymbol{\ge}` Rocky Linux (Green Obsidian 8.5)
+
+Installation
+------------
+
+The easiest way to get Samtools is to clone the git repository straight from GitHub:
+
+#. Copy the  files into a cluster location
+
+   .. code-block:: bash
+
+      $ git clone https://github.com/samtools/samtools
+
+
+
+#. Get Dependencies:
+
+At least the following are required:
+
+    GNU make
+    C compiler (e.g. gcc or clang)
+
+In addition, building the configure script requires:
+
+    autoheader
+    autoconf
+    autoreconf
+
+Running the configure script uses awk, along with a number of
+standard UNIX tools (cat, cp, grep, mv, rm, sed, among others).  Almost
+all installations will have these already.
+
+
+HTSlib uses the following external libraries.  Building requires both the
+library itself, and include files needed to compile code that uses functions
+from the library.  Note that some Linux distributions put include files in
+a development ('-dev' or '-devel') package separate from the main library.
+
+    zlib       (required)
+    libbz2     (required, unless configured with --disable-bz2)
+    liblzma    (required, unless configured with --disable-lzma)
+    libcurl    (optional, but strongly recommended)
+    libcrypto  (optional for Amazon S3 support; not needed on MacOS)
+    libdeflate (optional, but strongly recommended for faster gzip)
+
+
+
+
+htslib requires CMake (version >= 3.0). If you are missing CMake or have an older version, check your OS package manager (for Linux users) or download it here: http://www.cmake.org/cmake/resources/software.html .
+    .. code-block:: bash
+        $ cmake --version
+
+#. Ok, now that you have CMake ready to go, let's build Hts. A good practice in building applications is to do an out-of-source build, meaning that we're going to set up an isolated place to hold all the intermediate installation steps. In the top-level directory of BamTools, type the following commands:.
+
+    .. code-block:: bash
+
+        $ ./configure
+        $ cd /share/apps/samtools/1.20.0/gcc-11.2.0/
+        $ cmake
+
+
+
+#. After running cmake, just run:
+
+
+    .. code-block:: bash
+        $ sudo make prefix=/share/apps/samtools/1.20.0/gcc-11.2.0/ install
+
+
+
+
+
+
+
+References
+----------
+
+.. [1] Twelve years of SAMtools and BCFtools
+Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li
+GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008
+
+
+
+Authors
+-------
+
+- Isis Amaya <[email protected]>
+- Santiago Arias <[email protected]>

docs/source/software/applications/bamtools/bamtools-2.5.2/index.rst

@@ -10,11 +10,17 @@ BAMTOOLS 2.5.2
 
 Basic information
 ------------------
-
+- **Installation Date:** 17/06/2024
 - **Official Website:** https://github.com/pezmaster31/bamtools/wiki
 - **Installed on:** :ref:`Apolo II <about_apolo-ii>`
-
+- **License:** Apolo License
+
+Dependencies
+------------
 
+- gcc-11.2.0
+- samtools
+- htslib
 
 Tested on (Requirements)
 ------------------------
@@ -57,7 +63,7 @@ BamTools requires CMake (version >= 3.0). If you are missing CMake or have an ol
 
 #. After running cmake, just run:
 
-  
+
     .. code-block:: bash
         $ make install
 
@@ -71,7 +77,7 @@ References
 ----------
 
 .. [1] Bamtools Github Repository.
-       Retrieved June 18, 2024, from https://github.com/pezmaster31/bamtools 
+       Retrieved June 18, 2024, from https://github.com/pezmaster31/bamtools