... | ... | @@ -45,7 +45,7 @@ Ensure you have the following binaries available: |
|
|
Your directory structure should look like this after installation:
|
|
|
```
|
|
|
.
|
|
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\------- bioperl-1.2.3
|
|
|
\------- bioperl-1.6.924
|
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\------- ensembl
|
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\------- ensembl-compara
|
|
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\------- ensembl-external
|
... | ... | @@ -103,17 +103,17 @@ We will partially work through the second document to install the API. |
|
|
Use one of the following commands to get BioPerl
|
|
|
|
|
|
```bash
|
|
|
wget https://github.com/bioperl/bioperl-live/archive/bioperl-release-1-6-9.tar.gz
|
|
|
wget https://github.com/bioperl/bioperl-live/archive/release-1-6-924.tar.gz
|
|
|
```
|
|
|
|
|
|
```bash
|
|
|
curl -o bioperl-1.6.9.tar.gz https://github.com/bioperl/bioperl-live/archive/bioperl-release-1-6-9.tar.gz
|
|
|
curl -o release-1.6.924.tar.gz https://github.com/bioperl/bioperl-live/archive/release-1-6-924.tar.gz
|
|
|
```
|
|
|
|
|
|
Now untar
|
|
|
|
|
|
```bash
|
|
|
tar zxvf bioperl-1.6.9.tar.gz
|
|
|
tar zxvf bioperl-1.6.924.tar.gz
|
|
|
```
|
|
|
|
|
|
### Installing Ensembl API from Tarball
|
... | ... | @@ -178,7 +178,7 @@ git clone https://github.com/Ensembl/ensembl-rest.git |
|
|
Using bash we bring each modules directory onto the library path:
|
|
|
|
|
|
```bash
|
|
|
PERL5LIB=${PWD}/bioperl-1.6.9:${PERL5LIB}
|
|
|
PERL5LIB=${PWD}/bioperl-1.6.924:${PERL5LIB}
|
|
|
PERL5LIB=${PWD}/ensembl/modules:${PERL5LIB}
|
|
|
PERL5LIB=${PWD}/ensembl-compara/modules:${PERL5LIB}
|
|
|
PERL5LIB=${PWD}/ensembl-variation/modules:${PERL5LIB}
|
... | ... | |