{"repo":"Ensembl/ensembl-compara","free":true,"listed":false,"github":"https://github.com/Ensembl/ensembl-compara","clone":"git clone https://github.com/Ensembl/ensembl-compara.git","description":"The Ensembl Compara Perl API and SQL schema","language":"Perl","stars":56,"topics":["ensembl","perl","api","comparative-genomics","mysql","database","bioinformatics"],"license":"Apache-2.0","category":"databases-storage","readme_excerpt":"Ensembl Compara API The Ensembl Compara API (Application Programme Interface) serves as a middle layer between the underlying MySQL database and the user's script. It aims to encapsulate the database layout by providing high level access to the database. Find more information (including the installation guide and a tutorial) on the Ensembl website: See the Ensembl core repository for the guidelines on user contributions. Installation Perl modules We use a number of Perl modules that are all available on CPAN. We recommend using cpanminus to install these. You will need both the Core API dependencies and ours. API to access HAL alignments (progressive-Cactus) If working with HAL files, additional setup is required. There are several ways of installing the dependencies. Complete installation of progressive-Cactus Follow this procedure if you intend to run the cactus aligner. If Cactus is already installed on your system, you can directly jump to the section about setting up the API. Otherwise, do this: git clone https://github.com/glennhickey/progressiveCactus.git cd progressiveCactus # Make sure we use the latest version git pull # Download the dependencies git submodule update --init # We specifically need a more recent version of \"hal\" cd submodules/hal/ git checkout master git pull cd ../.. cd submodules/sonLib # edit include.mk and add \" -fPIC\" at the end of the cflags opt line (line 44) cd ../.. # Compile make # Check it passes the test-suite. You should see \"Result: PASS","default_branch":null,"files":null,"tree":[],"storefront":"/r/Ensembl","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/Ensembl/ensembl-compara/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}