... | ... | @@ -53,6 +53,7 @@ Your directory structure should look like this after installation: |
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\------- ensembl-rest
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\------- ensembl-tools
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\------- ensembl-variation
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\------- ensembl-io
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```
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## Installing Catalyst
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... | ... | @@ -97,22 +98,22 @@ Should you already have an Ensembl API for the required release then skip to "In |
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We will partially work through the second document to install the API.
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### Installing BioPerl 1.2.3
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### Installing BioPerl 1.6.9
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Use one of the following commands to get BioPerl
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```bash
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wget http://bioperl.org/DIST/old_releases/bioperl-1.2.3.tar.gz
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wget https://github.com/bioperl/bioperl-live/archive/bioperl-release-1-6-9.tar.gz
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```
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```bash
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curl -o bioperl-1.2.3.tar.gz http://bioperl.org/DIST/old_releases/bioperl-1.2.3.tar.gz
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curl -o bioperl-1.6.9.tar.gz https://github.com/bioperl/bioperl-live/archive/bioperl-release-1-6-9.tar.gz
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```
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Now untar
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```bash
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tar zxvf bioperl-1.2.3.tar.gz
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tar zxvf bioperl-1.6.9.tar.gz
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```
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### Installing Ensembl API from Tarball
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... | ... | @@ -124,6 +125,29 @@ wget ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz |
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tar zxvf ensembl-api.tar.gz
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```
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### Installing Tabix
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New components of the REST API require the [Tabix](https://github.com/samtools/tabix) library. To do so run the following code.
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```bash
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wget https://github.com/samtools/tabix/archive/master.tar.gz
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tar zxf master.tar.gz
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(cd tabix-master && make)
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(cd tabix-master/perl && perl Makefile.PL && make)
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```
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In addition add the following lines to your environment:
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```
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TABIX_HOME=path/to/tabix
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PERL5LIB=${PERL5LIB}:${TABIX_HOME}/perl/blib/lib:${TABIX_HOME}/perl/blib/arch
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export PERL5LIB
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# Setup LD_LIBRARY_PATH
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LD_LIBRARY_PATH=${TABIX_HOME}
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export LD_LIBRARY_PATH
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```
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## Installing the REST API
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### Installing from Git
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... | ... | @@ -139,7 +163,7 @@ git clone https://github.com/Ensembl/ensembl-rest.git |
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Using bash we bring each modules directory onto the library path:
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```bash
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PERL5LIB=${PWD}/bioperl-1.2.3:${PERL5LIB}
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PERL5LIB=${PWD}/bioperl-1.6.9:${PERL5LIB}
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PERL5LIB=${PWD}/ensembl/modules:${PERL5LIB}
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PERL5LIB=${PWD}/ensembl-compara/modules:${PERL5LIB}
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PERL5LIB=${PWD}/ensembl-variation/modules:${PERL5LIB}
|
... | ... | @@ -147,6 +171,8 @@ Using bash we bring each modules directory onto the library path: |
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export PERL5LIB
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```
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*Remember to bring Tabix onto your PERL5LIB as described above*
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### Setting up Catalyst and Ensembl REST using cpanm
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First cd into the directory:
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... | ... | |