Download File As6.zip
Bowtie and Bowtie 2 are read aligners for sequencing reads. Bowtie specializes in short reads, generally about 50bp or shorter. Bowtie 2 specializes in longer reads, up to around hundreds of base pairs. HTTPS URLs allow you to download the files from your web browser or using command-line tools like wget or curl. The S3 URLs can be used with AWS tools, including the AWS console and AWS command-line interface.
Download File As6.zip
In the past, Bowtie 1 & 2 had incompatible genome indexes. This changed in July 2019 when Bowtie v1.2.3 gained the ability to use Bowtie 2 formatted genome indexes (ending in .bt2). We list only Bowtie 2-format .bt2 index files here.
You can download all the files for a given assembly as a single zip file, or as 6 separate .bt2 files. For example, if you only need the forward version of the genome index (e.g. for exact matching only), you can download the files individually and omit the .rev.1.bt2 and .rev.2.bt2 files. Downloading already-decompressed index files might also be quicker for applications running in the AWS cloud.
p.p1 margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica JBoss Application Server downloads starting from version 7.0 are hosted on jboss.org. Prior to version 7.0 they are hosted on sourceforge.net. For copyright purposes, a detailed source code change log is stored in the .log file.
If you're importing addresses from an external file, you may notice that the leading zeros in postal codes disappear. That's because Excel interprets the column of postal code values as numbers, when what you really need is for them to be stored and formatted as text. To solve this problem, in step 3 of the Text Import Wizard, click the column containing postal codes, and then, under Column data format, click Text. Click Finish to finish importing your data.
JBoss AS7 is structured differently from previous versions of JBoss AS, so you may want do a little research before you attempt to migrate your application. Getting Started with JBoss Application Server 7 in the Getting Started Guide has a lot of useful information, including a table that lists the Java Enterprise Edition 6 Web Profile features that are supported in AS 7.0. If your application uses features that go beyond the Web Profile specification, you must use release AS 7.1 or later as it supports the EE6 Full Profile. You should also read Getting started with JBoss AS for helpful information about how to install and run the application server.
Even though in AS7 modules are isolated by default, as part of the deployment process some dependencies on modules defined by the application server are set up for you automatically. For instance, if you are deploying a Java EE application, a dependency on the Java EE API's will be added to your module automatically. Similarly if your module contains a beans.xml file, a dependency on Weld will be added automatically, along with any supporting modules that weld needs to operate. For a complete list of the automatic dependencies that are added see Implicit module dependencies for deployments.
Depending on which components your application uses, you may need to add one or more dependencies to this file. There is more information about these dependencies in the following paragraphs.The following is an example of MANIFEST.MF file that has been modified to contain dependencies and classpath entries:
This file is a JBoss specific deployment descriptor that can be used to control class loading in a fine grained manner. Like the MANIFEST.MF, this file can be used to add dependencies. If can also prevent automatic dependencies from being added, define additional modules, change an EAR deployment's isolated class loading behaviour, and add additional resource roots to a module.
In previous versions of JBoss AS, you controlled the order of deployments within an EAR through the use of the jboss-app.xml file. This is no longer the case. The Java EE6 spec provides the element in the application.xml which allows control of the order in which the Java EE modules within an EAR are deployed.
In this case, the server is not able to determine that that EJB component is in the myBeans.jar and you need to enforce that the components in the myBeans.jar are initialized and started before the components in myApp.war. To do this, you set the element to true and specify the order of the myBeans.jar and myApp.war modules in the application.xml file.
The jboss-ejb3.xml deployment descriptor replaces the jboss.xml deployment descriptor to override and add to the features provided by the Java Enterprise Edition (EE) defined ejb-jar.xml deployment descriptor. The new file is incompatible with jboss.xml, and the jboss.xml is now ignored in deployments.
The login-config.xml file is no longer used for security configuration. Security is now configured in the element in the server configuration file. For a standalone server, this is the standalone/configuration/standalone.xml file. If you are running your server in a managed domain, this is the domain/configuration/domain.xml file.
Stop the server and open the server configuration file in a text editor. If you are running a standalone server, this is the EAP_HOME/standalone/configuration/standalone.xml file, or the EAP_HOME/domain/configuration/domain.xml file if you are running a managed domain.
In previous versions of the application server, the JCA data source configuration was defined in a file with a suffix of *-ds.xml. This file was then deployed in the server's deploy directory. The JDBC driver was copied to the server lib/ directory or packaged in the application's WEB-INF/lib/ directory.
In AS7, this has all changed. You will no longer package the JDBC driver with the application or in the server/lib directory. The *-ds.xml file is now obsolete and the datasource configuration information is now defined in the standalone/configuration/standalone.xml or in the domain/configuration/domain.xml file. The IronJacamar distribution features a migration tool that can help you convert your previous datasource configuration file into the new format. You can find more information about the tool here: IronJacamar Datasource and Resource Adapter Migration Tool .
A JDBC 4-compliant driver can be installed as a deployment or as a core module. A driver that is JDBC 4-compliant contains a META-INF/services/java.sql.Driver file that specifies the driver class name. A driver that is not JDBC 4-compliant requires additional steps, as noted below.
In AS7, a datasource is configured in the server configuration file. If you are running in domain mode, the configuration file is the domain/configuration/domain.xml file. If you are running in standalone mode, you will configure the datasource in the standalone/configuration/standalone.xml file. Schema reference information, which is the same for both modes, can be found here: Datasource Descriptors.
First, you will need to create a datasource element and a driver element for your JDBC driver and datasource information in the standalone.xml or domain.xml file. You will use some of the same information that was previously defined in the *-ds.xml file.
A JAR that is JDBC 4-compliant contains a META-INF/services/java.sql.Driver file that specifies the driver class name. This is used by the server to find name of the class(es) of the Drivers which exist in that JAR.
This is an example of the driver element for driver that is not JDBC 4-compliant. The driver-class must be specified since it there is no META-INF/services/java.sql.Driver file that specifies the driver class name.
Any JDBC 4-compliant driver will automatically be recognized and installed into the system by name and version. A JDBC 4-compliant JAR is identified using the Java service provider mechanism. It contains a text a file named "META-INF/services/java.sql.Driver", which contains the name of the class(es) of the Drivers which exist in that JAR. If your JDBC driver JAR is not JDBC 4-compliant, it can be made deployable by adding the java.sql.Driver file to the JAR or by deploying the JAR with an overlay. More information on that topic can be found here: Installing a JDBC Driver as a Deployment.
In AS7, a resource adapter is configured in the server configuration file. If you are running in domain mode, the configuration file is the domain/configuration/domain.xml file. If you are running in standalone mode, you will configure the resource adapter in the standalone/configuration/standalone.xml file. Schema reference information, which is the same for both modes, can be found here: Resource adapter descriptors. The IronJacamar distribution features a migration tool that can help you convert your previous datasource configuration file into the new format. You can find more information about the tool here: IronJacamar Datasource and Resource Adapter Migration Tool .
- the application name of the deployed EJBs. This is typically the ear name without the .ear suffix, however, the name can be overridden in the application.xml file. If the application is not deployed as a .ear, this value is an empty string. Assume this example was not deployed as an EAR.
If your application contains a persistence.xml file or the code uses @PersistenceContext or @PersistenceUnit, AS7 will detect this during deployment and assume the application uses JPA. It will implicitly add Hibernate 4 and a few other dependencies to your application classpath.
Hibernate "text" type now maps to JDBC LONGVARCHARIn pre-3.5 versions of Hibernate, text type were mapped to JDBC CLOB. A new Hibernate type, "materialized_clob", was added to map Java String properties to JDBC CLOB. If an application has properties configured as type="text" that are intended to be mapped to JDBC CLOB, they should be changed to type="materialized_clob" in hbm mapping files, or, if using annotations, @Type(type = "text") should be replaced by @Lob.
AnnotationConfigration must be merged into ConfigurationAside from the fact that AnnotationConfiguration is now deprecated, this usually is not of concern. However, if you are still using an hbm.xml file, you should be aware that AS7 now uses the org.hibernate.cfg.EJB3NamingStrategy in AnnotationConfigration instead of the older org.hibernate.cfg.DefaultNamingStrategy that was previously used in Configuration. This can result in naming mismatches. If you rely on the naming strategy to default the name of a association (many-to-many and collections of elements) table, you may see this issue. To resolve it, you can tell Hibernate to use the the legacy org.hibernate.cfg.DefaultNamingStrategy by calling Configuration#setNamingStrategy and passing it org.hibernate.cfg.DefaultNamingStrategy#INSTANCE 041b061a72