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andreasprlic merged 3 commits into from
Feb 12, 2015
Merged

Updating tutorial to biojava 4 #4

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a8fac6a
Updating to biojava 4. Fixing biojava/bio/structure/* links to API docs
josemduarte Feb 11, 2015
c499da8
Now really fixing biojava.bio.structure.* links
josemduarte Feb 11, 2015
d6025cf
Fixing org.biojava3.* api docs links
josemduarte Feb 11, 2015
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Updating to biojava 4. Fixing biojava/bio/structure/* links to API docs
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@josemduarte
josemduarte committed Feb 11, 2015
commit a8fac6a3da26ebdbdea37e35ab133c4670168c8a
21 changes: 3 additions & 18 deletions alignment/installation.md
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Expand Up @@ -6,22 +6,7 @@ BioJava is open source and you can get the code from [Github](https://github.com

BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.

Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .

You can add the BioJava repository by adding the following XML to your project pom.xml file:

```xml
<repositories>
...
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
</repository>
</repositories>
```

We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:

```xml
<dependencies>
Expand All @@ -31,8 +16,8 @@ We are currently in the process of changing our distribution to Maven Central, w
<dependency>

<groupId>org.biojava</groupId>
<artifactId>biojava3-core</artifactId>
<version>3.0.8</version>
<artifactId>biojava-alignment</artifactId>
<version>4.0.0</version>
</dependency>


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20 changes: 3 additions & 17 deletions core/installation.md
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Expand Up @@ -6,22 +6,8 @@ BioJava is open source and you can get the code from [Github](https://github.com

BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.

Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .

You can add the BioJava repository by adding the following XML to your project pom.xml file:

```xml
<repositories>
...
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
</repository>
</repositories>
```

We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:

```xml
<dependencies>
Expand All @@ -31,8 +17,8 @@ We are currently in the process of changing our distribution to Maven Central, w
<dependency>

<groupId>org.biojava</groupId>
<artifactId>biojava3-core</artifactId>
<version>3.0.8</version>
<artifactId>biojava-core</artifactId>
<version>4.0.0</version>
</dependency>


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25 changes: 5 additions & 20 deletions installation.md
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Expand Up @@ -6,22 +6,7 @@ BioJava is open source and you can get the code from [Github](https://github.com

BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.

Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .

You can add the BioJava repository by adding the following XML to your project pom.xml file:

```xml
<repositories>
...
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
</repository>
</repositories>
```

We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:

```xml
<dependencies>
Expand All @@ -31,8 +16,8 @@ We are currently in the process of changing our distribution to Maven Central, w
<dependency>

<groupId>org.biojava</groupId>
<artifactId>biojava3-genomics</artifactId>
<version>3.0.8</version>
<artifactId>biojava-genomics</artifactId>
<version>4.0.0</version>
<!-- note: the genomics module depends on the BioJava-core module and will import it automatically -->
</dependency>

Expand All @@ -44,8 +29,8 @@ We are currently in the process of changing our distribution to Maven Central, w
<dependency>

<groupId>org.biojava</groupId>
<artifactId>biojava3-structure</artifactId>
<version>3.0.8</version>
<artifactId>biojava-structure</artifactId>
<version>4.0.0</version>
</dependency>
</dependencies>
```
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19 changes: 5 additions & 14 deletions structure/installation.md
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Expand Up @@ -6,32 +6,23 @@ BioJava is open source and you can get the code from [Github](https://github.com

BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.

We are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:

You can add the BioJava repository by adding the following XML to your project pom.xml file:
```xml
<repositories>
...
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
</repository>
</repositories>
<dependencies>
...
<dependency>
<!-- This imports the latest SNAPSHOT builds from the protein structure modules of BioJava.
-->
<groupId>org.biojava</groupId>
<artifactId>biojava3-structure</artifactId>
<version>3.0.8</version>
<artifactId>biojava-structure</artifactId>
<version>4.0.0</version>
</dependency>
<!-- if you want to use the visualisation tools you need also this one: -->
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-structure-gui</artifactId>
<version>3.0.8</version>
<artifactId>biojava-structure-gui</artifactId>
<version>4.0.0</version>
</dependency>
<!-- other biojava jars as needed -->
</dependencies>
Expand Down