RAMPART | A configurable de novo assembly pipeline | Genomics library

 by   TGAC Java Version: Release-0.12.2 License: GPL-3.0

kandi X-RAY | RAMPART Summary

kandi X-RAY | RAMPART Summary

RAMPART is a Java library typically used in Artificial Intelligence, Genomics applications. RAMPART has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

RAMPART is a configurable pipeline for de novo assembly of DNA sequence data. RAMPART is not a de novo assembler. There are already many very good freely available assembly tools, however, few will always produce a good assembly first time using the default settings. Sometimes one particular assembler may perform well on your data and genome, but in other cases another performs better. Sometimes an assembly will be better if the reads are error corrected, other times not. Also depending on the data available, it maybe possible to improve the assembly with additional scaffolding or gap filling steps. There are many combinations of tools that could be tried and no clear way of knowing a priori, which will work best. RAMPART can be though of as a framework for these kinds of assembly projects. It is pipeline makes use of tried and tested tools for read pre-processing, assembly and assembly improvement, that allows the user to configure these tools and specify how they should be executed in a single configuration file. RAMPART also provides options for comparing and analysing sequence data and assemblies.

            kandi-support Support

              RAMPART has a low active ecosystem.
              It has 27 star(s) with 7 fork(s). There are 8 watchers for this library.
              It had no major release in the last 12 months.
              There are 16 open issues and 17 have been closed. On average issues are closed in 84 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of RAMPART is Release-0.12.2

            kandi-Quality Quality

              RAMPART has 0 bugs and 0 code smells.

            kandi-Security Security

              RAMPART has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              RAMPART code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              RAMPART is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              RAMPART releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              RAMPART saves you 5135 person hours of effort in developing the same functionality from scratch.
              It has 10795 lines of code, 1032 functions and 85 files.
              It has medium code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed RAMPART and discovered the below as its top functions. This is intended to give you an instant insight into RAMPART implemented functionality, and help decide if they suit your requirements.
            • Run a sample
            • Gets all the fasta files in the specified directory
            • Sets the optimal kmer values based on the given kmer configuration file
            • Load the optimal kmer map
            • Computes an AssemblyStats for the given analysis
            • Returns a string representation of the matrix
            • Returns a string representation of this object
            • Returns a string representation of this assembly
            • Parses the given XML element
            • Updates the query stats for a table
            • Dispatches the AMP stage
            • Load weightings
            • Run a MECQ sample
            • Main entry point
            • Execute a MASSQ sample
            • Executes the given assembly
            • Entry point for the report
            • Performs sample analysis
            • Process all samples
            • Parse the options from the command line
            • Runs a sample
            • Start the stats
            • Validates the sample output
            • Executes a MECQ sample
            • Executes a sample
            • Process the job
            Get all kandi verified functions for this library.

            RAMPART Key Features

            No Key Features are available at this moment for RAMPART.

            RAMPART Examples and Code Snippets

            No Code Snippets are available at this moment for RAMPART.

            Community Discussions


            Apache Rampart WS-Security: one client, several service instances
            Asked 2021-Jun-10 at 14:52

            I'm adding X.509 Mutual Certificate authentication into the project. The specific case here is that one client (let's say manager) can access several service instances (servers). Each server has its own certificate. When providing a policy.xml configuration on client side should be set to server's alias certificate stored in client's trustore. It's not a problem when the server is only one but when client need to access specific server, an appropriate server's public key should be used for encryption so I need to provide a proper alias from the truststore. I was thinking to programmarically change Rampart configuration on each request to set a specific alias name but this looks like not a proper way to do. I'm looking for a standard approach here or, perhaps, some way to configure that in policy.xml My client's (manager's) Rampart configuration part from policy.xml is below



            Answered 2021-Jun-10 at 14:52

            This problem was resolved by programmatically setting encryptionUser parameter to already parsed and built (from policy.xml) RampartConfig object inside Policy object. Build Policy object from configuration file, then go through the Assertions, find RamparConfig object among them and set the property.

            Source https://stackoverflow.com/questions/66113823


            how to display cities in one dropdown based on selected state in other dropdown using json data in angular ionic?
            Asked 2021-Apr-27 at 16:44

            following are my files for html, .ts and json . As json data was very extensive therefore i have just added a few states and their cities. my 1st dropdown is showing all states. Now I want to match my 1st dropdown's selected value of state with a key "state" in "cities" object in my json file so i can populate 2nd dropdown with cities relevant to that state. and I want to do this in function "getCitiesForSelectedState". please help me find solution for this.

            //.ts file



            Answered 2021-Apr-27 at 16:44

            You can do it with the $event parameter. Make sure to compare your values safely.

            If your value is not in the right type or has spaces or unwanted chars, this c.state == val might not work.

            You can use the trim function to compare your value safely: c.state.trim() == val.trim()


            Source https://stackoverflow.com/questions/67284495


            Firestore Get all Documents and Display as HTML Table on Google App Script Web App
            Asked 2021-Apr-19 at 05:26

            Thank you in advance.

            Need help on using FirestoreGoogleAppsScript library. Need to pull all documents and display on an HTML Table. I was able to use allDocumentsRows = firestore.getDocuments("StudentInfo"); but I'm getting several data not sure how to parse please see result below.

            Again thank you so much

            Below is my Firestore:



            Answered 2021-Apr-19 at 05:26

            I believe your goal as follows.

            • You want to retrieve the values from Firestore and you want to create a HTML table using the retrieved values using Google Apps Script.

            When the sample value of allDocumentsRows = firestore.getDocuments("StudentInfo") is the values in your question, and the header row is ["Age", "Fname", "Lname", "StudID", "Gender"], the sample script is as follows.

            Sample script:

            Source https://stackoverflow.com/questions/67154953


            Axis2 1.6.4 to 1.7.9 - AxisFault: The service cannot be found for the endpoint reference (EPR)
            Asked 2021-Mar-30 at 09:55

            I want to switch from Axis2 1.6.4 to 1.7.9 due to various circumstances. the pom.xml and axis2.xml have been adjusted accordingly (by the Apache Migration Guide). Previously I build the project via Eclipse but now it should be build via maven. Axis2 is embedded into the project via maven-war-plugin.

            Now I can't get the Endpoint to show up like before the switch to 1.7.9 . Your help would be much appreciated.

            My Endpoint should be: https://localhost:8443/SoapEndpoint/services/MainService.MainServiceHttpsSoap11Endpoint/

            Edit: I also switched from Java 8 to 11




            Answered 2021-Mar-30 at 09:55

            After some research and help the solution has been found:

            There appeared a breaking change in Axis2 1.7.0 (https://issues.apache.org/jira/browse/AXIS2-5340)

            Adding the following lines to the axis2.xml fixed the problem for me:

            Source https://stackoverflow.com/questions/66766456


            axis2 client Trying to write END_DOCUMENT when document has no root (ie. trying to output empty document) error
            Asked 2020-May-24 at 15:42

            I have a legacy WebServiceProject which connects to ws-security enabled web service using axis2 & rampart.

            Here is my axis2.xml:



            Answered 2020-May-20 at 13:33

            I was using JDK 13, I switched back to JDK 8, and yes, it works!

            Source https://stackoverflow.com/questions/61913437


            wso2 ei invoking endpoint with signature
            Asked 2019-Mar-21 at 17:44

            i starting to use wso2EI in my company. We have a requirement to invoke a service that exposes ones of our provider. This service is a SOAP webservice with signature in body through a keystore (they send me a pfx) and the idea is to use the wso2EI to invoke that service to consume internaly through this application.

            So, I create a proxy service and the Policy.xml. When i try call the proxy service without the Policy.xml and i put a harcoded request it works fine. But when i put the Policy im facing the following error:

            [-1234] [] [PassThroughMessageProcessor-351] ERROR {org.apache.synapse.core.axis2.Axis2Sender} - Unexpected error during sending message out java.lang.NullPointerException at sun.security.provider.JavaKeyStore$JKS.convertAlias(JavaKeyStore.java:58) at sun.security.provider.JavaKeyStore.engineGetCertificateChain(JavaKeyStore.java:163) at sun.security.provider.JavaKeyStore$JKS.engineGetCertificateChain(JavaKeyStore.java:56) at sun.security.provider.KeyStoreDelegator.engineGetCertificateChain(KeyStoreDelegator.java:101) at sun.security.provider.JavaKeyStore$DualFormatJKS.engineGetCertificateChain(JavaKeyStore.java:70) at java.security.KeyStore.getCertificateChain(KeyStore.java:1048) at org.apache.ws.security.components.crypto.CryptoBase.getCertificates(CryptoBase.java:468) at org.apache.ws.security.message.WSSecSignature.prepare(WSSecSignature.java:313) at org.apache.rampart.builder.BindingBuilder.getSignatureBuilder(BindingBuilder.java:351) at org.apache.rampart.builder.BindingBuilder.getSignatureBuilder(BindingBuilder.java:266) at org.apache.rampart.builder.AsymmetricBindingBuilder.doSignature(AsymmetricBindingBuilder.java:762) at org.apache.rampart.builder.AsymmetricBindingBuilder.doSignBeforeEncrypt(AsymmetricBindingBuilder.java:457) at org.apache.rampart.builder.AsymmetricBindingBuilder.build(AsymmetricBindingBuilder.java:97) at org.apache.rampart.MessageBuilder.build(MessageBuilder.java:147) at org.apache.rampart.handler.RampartSender.invoke(RampartSender.java:65) at org.apache.axis2.engine.Phase.invokeHandler(Phase.java:340) at org.apache.axis2.engine.Phase.invoke(Phase.java:313) at org.apache.axis2.engine.AxisEngine.invoke(AxisEngine.java:261) at org.apache.axis2.engine.AxisEngine.send(AxisEngine.java:426) at org.apache.synapse.core.axis2.DynamicAxisOperation$DynamicOperationClient.send(DynamicAxisOperation.java:185) at org.apache.synapse.core.axis2.DynamicAxisOperation$DynamicOperationClient.executeImpl(DynamicAxisOperation.java:167) at org.apache.axis2.client.OperationClient.execute(OperationClient.java:149) at org.apache.synapse.core.axis2.Axis2FlexibleMEPClient.send(Axis2FlexibleMEPClient.java:603) at org.apache.synapse.core.axis2.Axis2Sender.sendOn(Axis2Sender.java:85) at org.apache.synapse.core.axis2.Axis2SynapseEnvironment.send(Axis2SynapseEnvironment.java:547) at org.apache.synapse.endpoints.AbstractEndpoint.send(AbstractEndpoint.java:384) at org.apache.synapse.endpoints.AddressEndpoint.send(AddressEndpoint.java:65) at org.apache.synapse.mediators.builtin.SendMediator.mediate(SendMediator.java:123) at org.apache.synapse.mediators.AbstractListMediator.mediate(AbstractListMediator.java:108) at org.apache.synapse.mediators.AbstractListMediator.mediate(AbstractListMediator.java:70) at org.apache.synapse.mediators.base.SequenceMediator.mediate(SequenceMediator.java:158) at org.apache.synapse.core.axis2.ProxyServiceMessageReceiver.receive(ProxyServiceMessageReceiver.java:224) at org.apache.axis2.engine.AxisEngine.receive(AxisEngine.java:180) at org.apache.synapse.transport.passthru.ServerWorker.processEntityEnclosingRequest(ServerWorker.java:415) at org.apache.synapse.transport.passthru.ServerWorker.run(ServerWorker.java:151) at org.apache.axis2.transport.base.threads.NativeWorkerPool$1.run(NativeWorkerPool.java:172) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

            The proxy is:


            and the policy:

            JKS xx/xx/xx/certificado.jks xxx


            After setting the org.apache.synapse.transport.http.wire with DEBUG option i started to view the resoponse in the log but the servirce continues failing. The error is this:

            [2019-03-19 16:29:29,620] [-1] [] [PassThroughMessageProcessor-2] ERROR {org.apache.axis2.transport.base.threads.NativeWorkerPool} - Uncaught exception java.lang.NullPointerException at org.apache.ws.security.processor.SignatureProcessor.verifyXMLSignature(SignatureProcessor.java:265) at org.apache.ws.security.processor.SignatureProcessor.handleToken(SignatureProcessor.java:124) at org.apache.ws.security.WSSecurityEngine.processSecurityHeader(WSSecurityEngine.java:332) at org.apache.ws.security.WSSecurityEngine.processSecurityHeader(WSSecurityEngine.java:249) at org.apache.rampart.RampartEngine.process(RampartEngine.java:221) at org.apache.rampart.handler.RampartReceiver.invoke(RampartReceiver.java:93) at org.apache.axis2.engine.Phase.invokeHandler(Phase.java:340) at org.apache.axis2.engine.Phase.invoke(Phase.java:313) at org.apache.axis2.engine.AxisEngine.invoke(AxisEngine.java:261) at org.apache.axis2.engine.AxisEngine.receive(AxisEngine.java:167) at org.apache.synapse.transport.passthru.ClientWorker.run(ClientWorker.java:263) at org.apache.axis2.transport.base.threads.NativeWorkerPool$1.run(NativeWorkerPool.java:172) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

            The proxy server is still the same.

            UPDATE 2 Finally i made it !!!. The problem were in the proxy service and the security mediator. Here is the final proxy service. Thanks to all!!:




            Answered 2019-Mar-15 at 14:06

            Two things stand out to me: It seems, based on the error, that you have some keystore or certificate alias issue. A few things to try:

            • A common mistake is to import the certificate without aliasname. Inspect the keystore to see if the name is correct.
            • I do not see a callbackhandler mentioned? Did you implement one?

            Some more info here including an examplepolicy and callbackhandler project

            Source https://stackoverflow.com/questions/55183964


            WSO2 ESB - Rampart Password Callback class - WSPasswordCallback cannot be cast
            Asked 2019-Jan-11 at 09:54

            I want to to invoke a secured backend service in WSO2 ESB 5.0.0 with rampart configuration and Password Callback class



            Answered 2018-Dec-25 at 23:32

            Have a look at the available version of wss4j inside "wso2esb-5.0.0/repository/components/plugins" folder. It looks like you are using a different version in the compile time, that may lead to this kind of issue.

            Try to use wss4j with the following dependency version when compiling.

            Source https://stackoverflow.com/questions/53925400


            Loading Content On New View Controller
            Asked 2018-Dec-10 at 07:13

            In my main view controller i have code that will take u to another page once the camera identifies something and you tap on the screen:



            Answered 2018-Dec-10 at 01:40

            My guess is that one of these names is wrong:

            Source https://stackoverflow.com/questions/53697735


            WSO2 ESB consuming WCF Secured Method with certificate
            Asked 2017-Dec-21 at 19:59

            I'm new in WSO2 ESB. I've built a wcf service with wsHttpBinding secured with self certificate. and I cannot find a way to integrate that service with ESB. Any Suggestions please?

            I created a self signed certificate using makecert command but I cannot configure the rampart to use the created certificate. how can I do that? I've got lost. my wsHttpBinding looks like this:



            Answered 2017-Dec-21 at 19:59

            I figured it out, It seems that the problem is that there is an issue when using SSLContextToken because the axis2 does not understand the that so I changed the wsHttpBinding like this:

            Source https://stackoverflow.com/questions/47820442


            Spring Boot startup fail after adding Axis 2 client dependencies
            Asked 2017-Oct-27 at 06:03

            I am developing a demo application for consuming a Soap Web Service and I am using axis 2 as client. I decided to use Spring boot and merge my code into it. At first the simple Spring Boot was completely Ok and I could create a demo jsp page and a couple of rest webservices. After I added stub code jar files and also the Axis and Rampart dependencies into pom.xml it keeps getting error at startup.

            Here is an snippet code for pom.xml the issue is easily replicable by just adding



            Answered 2017-Oct-27 at 06:03

            The issue was a transitive dependency "javax.servlet:servlet-api" that comes with "org.apache.axis2:axis2-metadata".

            I fixed that by excluding it from the axis2 and rampart dependencies:

            Source https://stackoverflow.com/questions/46967606

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network


            No vulnerabilities reported

            Install RAMPART

            There are three ways to install RAMPART: using homebrew, from tarball, and from source code. All installation methods require you to have JRE V1.7+ installed. For more detailed installation instructions please consult the RAMPART manual. To install from homebrew, please first ensure you have homebrew or linuxbrew installed and the homebrew science repo tapped. Then simply type: ``brew install rampart``. To install from tarball please go to the releases section of the RAMPART github page: ``https://github.com/TGAC/RAMPART/releases`` Then extract to a directory of your choice: ``tar -xvf <name_of_tarball>``.
            Maven 3
            JDK v1.7+
            Sphinx and texlive (If you would like to compile the manual. If these are not installed you must comment out the create-manual execution element from the pom.xml file.))
            Some common errors the user may encounter, and steps necessary to fix the, during the installation procedure follow:. ``Exception in thread "main" java.lang.UnsupportedClassVersionError: uk/ac/tgac/rampart/RampartCLI : Unsupported major.minor version 51.0``. This occurs When trying to run RAMPART, or any associated tools, with an old JRE version. If you see this, install or load JRE V1.7 or later and try again. Note that if you are trying to compile RAMPART you will need JDK (Java Development Kit) V1.7 or higher as well. If you are compiling RAMPART from source, if you encounter a problem when creating the documention with sphinx it maybe that your sphinx version is different from what is expected. Specifically please check that your sphinx configuration provides a tool called ``sphinx_build`` and that tool is available on the PATH. Some sphinx configurations may have an executable named like this ``sphinx_build_<version>``. If this is the case you can try making a copy of this executable and remove the version suffix from it. Alternatively if you do not wish to compile the documentation just remove it by commenting out the ``create-manual`` element from the pom.xml file. ``“[ERROR] Failed to execute goal org.apache.maven.plugins:maven-antrun-plugin:1.7:run (create-manual) on project rampart: An Ant BuildException has occured: Warning: Could not find file RAMPART.pdf to copy.” Creating an empty RAMPART.pdf file in the specified directory fixed this issue, allowing RAMPART to successfully build``. This error occurs because the RAMPART.pdf file was not created when trying to compile the documentation. RAMPART.pdf is created from the documentation via sphinx and texlive. If you see this error then probably sphinx is working fine but texlive is not installed. Properly installing and configuring texlive so it’s available on your path should fix this issue. Alternatively if you do not wish to compile the documentation just remove it by commenting out the ``create-manual`` element from the pom.xml file.
            Old Java Runtime Environment (JRE) installed:
            Incorrect sphinx configuration:
            Texlive not installed:


            Daniel Mapleson - Analysis Pipelines Project Leader at The Genome Analysis Centre (TGAC).
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