Doc/dorado

docs/source/software/applications/Geant4/11.1.2/index.rst

@@ -0,0 +1,117 @@
+.. _Geant4-11.1.2:
+
+
+GEANT4 11.1.2
+===========
+
+.. contents:: Table of Contents
+
+Basic information
+-----------------
+
+- **Official Website:** https://geant4.web.cern.ch/
+- **Downloads page:** https://geant4.web.cern.ch/download/
+- **Installed on:** APOLO II
+
+Tested on (Requirements)
+------------------------
+
+- **OS base:** Rocky Linux 8.5 (x86_64) :math:`\boldsymbol{\ge}` 8
+
+- **Compiler** GCC 9.3.0
+
+Installation
+-------------
+
+#. First of all, we need to load the following modules for the compilation
+
+    .. code-block:: bash
+
+        $ module load cmake-3.22.2-gcc-9.3.0-paiswui expat-2.4.6-gcc-9.3.0-nlngbc3 gcc/9.3.0 mpich/4.1_gcc-9.3.0
+
+#. Then, download the tar.gz file and unpack it
+
+    .. code-block:: bash
+
+        $ wget https://gitlab.cern.ch/geant4/geant4/-/archive/v11.1.2/geant4-v11.1.2.tar.gz
+        $ tar -xvf geant4-v11.1.2.tar.gz
+
+#. Then, we create two directories in the same location than we unpack the tar.gz file, one for build and the other for install
+
+    .. code-block:: bash
+
+        $ mkdir build_geant4 install_geant4
+
+
+#. Then we can continue with the installation
+
+    .. code-block:: bash
+
+        $ cd build_geant4
+        $ cmake -DCMAKE_INSTALL_PREFIX=../install -DGEANT4_BUILD_MULTITHREADED=ON ../geant4-v11.1.2/
+        $ make -j 8
+        $ make install
+
+.. note::
+
+    There is another flag for the cmake command, this flag is -DGEANT4_INSTALL_DATA. This flag for default is OFF and thanks to the firewall
+    of the University, this flag doesn't work, because it uses a protocol that this firewall doesn't allow. But you are free to try.
+
+#. Now, if we need to use the data, we must install this manually as follows
+
+    .. code-block:: bash
+
+        $ cd ../install_geant4/share/Geant4
+        $ mkdir data
+        $ cd data
+
+#. Then, we download the tar.gz files and unpack it
+
+    .. code-block:: bash
+
+        $ wget https://cern.ch/geant4-data/datasets/G4NDL.4.7.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4EMLOW.8.2.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4PhotonEvaporation.5.7.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4RadioactiveDecay.5.6.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4PARTICLEXS.4.0.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4PII.1.3.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4RealSurface.2.2.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4SAIDDATA.2.0.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4ABLA.3.1.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4INCL.1.0.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4ENSDFSTATE.2.3.tar.gz
+        $ wget https://cern.ch/geant4-data/datasets/G4TENDL.1.4.tar.gz
+        $ tar xf G4ABLA.3.1.tar.gz
+        $ tar xf G4EMLOW.8.2.tar.gz
+        $ tar xf G4ENSDFSTATE.2.3.tar.gz
+        $ tar xf G4INCL.1.0.tar.gz
+        $ tar xf G4NDL.4.7.tar.gz
+        $ tar xf G4PARTICLEXS.4.0.tar.gz
+        $ tar xf G4PII.1.3.tar.gz
+        $ tar xf G4RadioactiveDecay.5.6.tar.gz
+        $ tar xf G4RealSurface.2.2.tar.gz
+        $ tar xf G4SAIDDATA.2.0.tar.gz
+        $ tar xf G4TENDL.1.4.tar.gz
+
+.. note::
+
+    This process is very slow, so you must be patient.
+
+#. Then, we must modify one file to use this data
+
+    .. code-block:: bash
+
+        $ cd ../../../bin/
+        $ vim geant4.sh
+
+#. Now, we modify lines 70 - 80 (delete '#' to uncommon these lines). Then, we exit from vim and execute this file
+
+    .. code-block:: bash
+
+        $ ./geant4.sh
+
+#. Now we are ready to use Geant4.
+
+:Author:
+
+ - Juan Manuel Gómez <[email protected]>

docs/source/software/applications/Geant4/index.rst

@@ -0,0 +1,10 @@
+.. _ Geant4-index:
+
+GEANT4
+=====
+
+.. toctree::
+   :caption: Versions
+   :maxdepth: 1
+
+   11.1.2/index

docs/source/software/applications/ROOT/6/index.rst

@@ -0,0 +1,61 @@
+.. _ROOT-6:
+
+
+ROOT 6
+===========
+
+.. contents:: Table of Contents
+
+Basic information
+-----------------
+
+- **Official Website:** https://root.cern/
+- **Install page:** https://root.cern/install/
+- **Installed on:** APOLO II
+
+Tested on (Requirements)
+------------------------
+
+- **OS base:** Rocky Linux 8.5 (x86_64) :math:`\boldsymbol{\ge}` 8
+
+- **Compiler** GCC 9.3.0
+
+Installation
+-------------
+
+#. First of all, we need to load the following module for the compilation
+
+    .. code-block:: bash
+
+        $ module load python/3.9_miniconda-4.10.3
+
+#. Then, we create a conda environment
+
+    .. code-block:: bash
+
+        $ conda config --set channel_priority strict
+        $ conda create -c conda-forge --name <my-environment> root
+
+.. note::
+
+    Replace <my-environment> for a proper name for the environment.
+
+#. Then, we activate the environment in order to use ROOT
+
+    .. code-block:: bash
+
+        $ conda activate <my-environment>
+
+#. Now we are ready to use ROOT.
+
+    .. code-block:: bash
+
+        $ root
+
+.. note::
+
+    Always that we want to use ROOT, we must activate the environment.
+
+:Author:
+
+- Juan Manuel Gómez <[email protected]>

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

@@ -0,0 +1,10 @@
+.. _ ROOT-index:
+
+ROOT
+=====
+
+.. toctree::
+   :caption: Versions
+   :maxdepth: 1
+
+   6/index

docs/source/software/applications/dorado/0.3.4/index.rst

@@ -0,0 +1,51 @@
+.. _dorado-0.3.4:
+
+
+DORADO-0.3.4
+===========
+
+.. contents:: Table of Contents
+
+Basic information
+-----------------
+
+- **Install page:** https://github.com/nanoporetech/dorado/tree/master
+- **Installed on:** APOLO II
+
+Tested on (Requirements)
+------------------------
+
+- **OS base:** Rocky Linux 8.5 (x86_64) :math:`\boldsymbol{\ge}` 8
+
+- **Compiler** GCC 9.3.0
+
+Installation
+-------------
+
+#. First of all, we need to download the tar.gz file
+
+    .. code-block:: bash
+
+        $ wget wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.3.4-linux-x64.tar.gz
+
+#. Then, we unpack this tar.gz file
+
+    .. code-block:: bash
+
+        $ tar xf dorado-0.3.4-linux-x64.tar.gz
+
+#. Then, we enter in the dorado directory
+
+    .. code-block:: bash
+
+        $ cd dorado-0.3.4-linux-x64
+
+#. Now we are ready to use dorado
+
+    .. code-block:: bash
+
+        $ ./bin/dorado
+
+:Author:
+
+- Juan Manuel Gómez <[email protected]>

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

@@ -0,0 +1,10 @@
+.. _ dorado-index:
+
+DORADO
+=====
+
+.. toctree::
+   :caption: Versions
+   :maxdepth: 1
+
+   0.3.4/index

docs/source/software/applications/index.rst

@@ -90,3 +90,6 @@ and :ref:`Cronos <about_cronos>`) you can review the following entries:
    vsearch/index
    wps/index
    wrf/index
+   Geant4/index
+   ROOT/index
+   dorado/index