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    "# SeCaPr - Sequence Capture Processor\n",
    "A computational pipeline for processing Illumina sequence capture data\n",
    "\n",
    "***\n",
    "\n",
    "## Documentation\n",
    "The documentation, including an empirical data tutorial, is divided into the following steps (click on the links):\n",
    "- [Cleaning and adapter trimming](docs/notebook/cleaning_trimming.ipynb)\n",
    "- [De-novo contig assembly](docs/notebook/contig_assembly.ipynb)\n",
    "- [Extract target contigs](docs/notebook/extract_contigs.ipynb)\n",
    "- [Align contigs](docs/notebook/align_contigs.ipynb)\n",
    "- [Reference-based assembly](docs/notebook/reference_assembly.ipynb)\n",
    "- [Locus selection](docs/notebook/locus_selection.ipynb)\n",
    "- [Phasing alleles](docs/notebook/phasing.ipynb)\n",
    "\n",
    "***\n",
    "\n",
    "## Installation & Setup\n",
    "SeCaPr is available as a conda package on the bioconda channel. This makes installation very simple:\n",
    "\n",
    "### 1. Install conda\n",
    "\n",
    "Download the **Python2.7 version** of [Miniconda](https://conda.io/miniconda.html) and install it by executing the downloaded sh-file (see commands below). Conda is a software and environment manager, that makes installation of new software and of required dependencies very simple and straightforward.\n",
    "\n",
    "*Download conda:*\n",
    "<aside class=\"info\">\n",
    "*MacOS:*\n",
    "\n",
    "`wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh`;\n",
    "\n",
    "*Linux (64bit):*\n",
    "\n",
    "`wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh`;\n",
    "\n",
    "*Linux (32bit):*\n",
    "\n",
    "`wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86.sh`;\n",
    "</aside>\n",
    "\n",
    "\n",
    "*Install conda:*\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "`sh Miniconda2-latest-*.sh`\n",
    "</div>\n",
    "\n",
    "***\n",
    "\n",
    "### 2. Install the SECAPR environment\n",
    "Conda automatically downloads and installs all necessary software dependencies. We strongly recommend to **install SECAPR and all it's dependencies in a separate virtual environment**, in order to not interfer with potentially already installed verisons of the software dependencies.\n",
    "\n",
    "*Install SECAPR in virtual environment (here named `secapr_env`):*\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "`conda create -c bioconda -n secapr_env secapr`\n",
    "</div>\n",
    "\n",
    "Alternatively you can also just plainly install the software on your computer (without creating an environment) by clicking on the icon below and following the instructions (**not recommended!**):\n",
    "\n",
    "[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/secapr/README.html)\n",
    "\n",
    "***\n",
    "\n",
    "### 3. Activate the environment\n",
    "To activate the newly created environment, type:\n",
    "\n",
    "*Activate environment*:\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "`source activate secapr_env`\n",
    "</div>\n",
    "\n",
    "When the environment is activated, all the necessary software dependencies will be available in the standarad path, e.g. when you type `samtools` the samtools version required for SECAPR will be executed. After you are done using secapr, you can deactivate the environment to switch back to your standard environment with this command:\n",
    "\n",
    "*De-activate environment*:\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "`source deactivate`\n",
    "</div>\n",
    "\n",
    "***\n",
    "\n",
    "### 4. Check active environment\n",
    "Check if you are connected to the correct environment (there should eb a star in front of secapr_env in the output of this command):\n",
    "\n",
    "*Check active environment*:\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "`conda info --envs`\n",
    "</div>\n",
    "\n",
    "\n",
    "<div class=\"alert alert-block alert-warning\">IMPORTANT : When you are using hte SECAPR pipeline, make sure the secapr_env is activated. Activate with `source activate secapr_env`\n",
    "</div>\n",
    "\n",
    "***"
   ]
  }
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    "# SeCaPr - Sequence Capture Processor\n",
    "A computational pipeline for processing Illumina sequence capture data\n",
    "\n",
    "***\n",
    "\n",
    "## Documentation\n",
    "The documentation, including an empirical data tutorial, is divided into the following steps (click on the links):\n",
    "- [Cleaning and adapter trimming](docs/notebook/cleaning_trimming.ipynb)\n",
    "- [De-novo contig assembly](docs/notebook/contig_assembly.ipynb)\n",
    "- [Extract target contigs](docs/notebook/extract_contigs.ipynb)\n",
    "- [Align contigs](docs/notebook/align_contigs.ipynb)\n",
    "- [Reference-based assembly](docs/notebook/reference_assembly.ipynb)\n",
    "- [Locus selection](docs/notebook/locus_selection.ipynb)\n",
    "- [Phasing alleles](docs/notebook/phasing.ipynb)\n",
    "\n",
    "***\n",
    "\n",
    "## Installation & Setup\n",
    "SeCaPr is available as a conda package on the bioconda channel. This makes installation very simple:\n",
    "\n",
    "### 1. Install conda\n",
    "\n",
    "Download the **Python2.7 version** of [Miniconda](https://conda.io/miniconda.html) and install it by executing the downloaded sh-file (see commands below). Conda is a software and environment manager, that makes installation of new software and of required dependencies very simple and straightforward.\n",
    "\n",
    "**Download conda:**\n",
    "\n",
    "*MacOS:*\n",
    "\n",
    "<font color=green>\n",
    "wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh\n",
    "</font>\n",
    "\n",
    "*Linux (64bit):*\n",
    "\n",
    "`wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh`;\n",
    "\n",
    "*Linux (32bit):*\n",
    "\n",
    "`wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86.sh`;\n",
    "\n",
    "\n",
    "**Install conda:**\n",
    "\n",
    "`sh Miniconda2-latest-*.sh`\n",
    "\n",
    "***\n",
    "\n",
    "### 2. Install the SECAPR environment\n",
    "Conda automatically downloads and installs all necessary software dependencies. We strongly recommend to **install SECAPR and all it's dependencies in a separate virtual environment**, in order to not interfer with potentially already installed verisons of the software dependencies.\n",
    "\n",
    "*Install SECAPR in virtual environment (here named `secapr_env`):*\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "`conda create -c bioconda -n secapr_env secapr`\n",
    "</div>\n",
    "\n",
    "Alternatively you can also just plainly install the software on your computer (without creating an environment) by clicking on the icon below and following the instructions (**not recommended!**):\n",
    "\n",
    "[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/secapr/README.html)\n",
    "\n",
    "***\n",
    "\n",
    "### 3. Activate the environment\n",
    "To activate the newly created environment, type:\n",
    "\n",
    "*Activate environment*:\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "`source activate secapr_env`\n",
    "</div>\n",
    "\n",
    "When the environment is activated, all the necessary software dependencies will be available in the standarad path, e.g. when you type `samtools` the samtools version required for SECAPR will be executed. After you are done using secapr, you can deactivate the environment to switch back to your standard environment with this command:\n",
    "\n",
    "*De-activate environment*:\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "`source deactivate`\n",
    "</div>\n",
    "\n",
    "***\n",
    "\n",
    "### 4. Check active environment\n",
    "Check if you are connected to the correct environment (there should eb a star in front of secapr_env in the output of this command):\n",
    "\n",
    "*Check active environment*:\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "`conda info --envs`\n",
    "</div>\n",
    "\n",
    "\n",
    "<div class=\"alert alert-block alert-warning\">IMPORTANT : When you are using hte SECAPR pipeline, make sure the secapr_env is activated. Activate with `source activate secapr_env`\n",
    "</div>\n",
    "\n",
    "***"
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