The Samtools installation will follow the common configure, make, make install process: Basic Installation
There is also a README and INSTALL file availableįor HTSlib in the source code directory samtools-1.10/htslib-1.10/.Ĭd to samtools-1.10 and read through README and INSTALL. Recommend reviewing before compiling software. README files will always be included with your source code and we You will also see a README file in the source code directory which will provide The HTSlib website where the Samtools source code is hosted provides basic installation instructionsĪnd refers users to INSTALL (which is a plain text file that can be found in samtools-1.10/) for
In the installation instructions for your software which will be available online and/or Software? Answers to these questions, and other important information, should be available What steps need to be performed for our compilation? What system dependencies exist for our Take a moment to look at the content available The above two commands will create a directory named samtools-1.10 which contains all the codeĪnd instructions needed for compiling Samtools and HTSlib. Login in to your OSG Connect login nodeĪnd use wget to download the source code directly and extract the tarball: ~]$ wget ~]$ tar -xjf samtools-1.10.tar.bz2 Right-click on the Samtools source code link and copy the link location. What this means is 1.) HTSlib is a dependency of Samtools and 2.) the HTSlib source code is includedĮither download the Samtools source code to your computer and upload to your login node, or " uses HTSlib internally these source packages contain their own copies of htslib" On the download page is some important information to make note of: Theĭevelopment code is also available via GitHub at. Compile Samtools Without CRAM Support Step 1. Installed and most Samtools users are only working with BAM files which does not require CRAMĭo I need CRAM support for my work? CRAM is an alternative compressed sequence alignmentįile format to BAM. With CRAM support requires additional dependencies (aka libraries) that will also need to be Why two examples? Currently, to install Samtools Specifically, this guide provides two examples of compiling Samtools, one without CRAM file For a general introduction to softwareĬompilation in OSG Connect, please see Compiling Software for OSG Connect. However, the steps described in thisĮxample are applicable to many other software. Software for working with aligned sequencing data. This guide providesĪ detailed example of compiling software for use in OSG Connect.įor this example, we will be compiling Samtools which is a very common bioinformatics Read through installation instructions, continuedĮxample of Compilng Software For Use In OSG Connect Introductionĭue to the distributed nature of the Open Science Pool, you will always need toĮnsure that your jobs have access to the software that will be executed.