Issue with build

[caleblareau]

I tried running the installation from the README, and everything went smoothly until the last step(./gradlew clean jar), which gives:

FAILURE: Build failed with an exception.

* Where:
Build file '/data/aryee/caleb/bazam/bazam/groovy-ngs-utils/build.gradle' line: 76

* What went wrong:
A problem occurred evaluating project ':groovy-ngs-utils'.
> Could not resolve all files for configuration ':groovy-ngs-utils:compile'.
   > Could not resolve de.erichseifert.gral:gral-core:0.10.
     Required by:
         project :groovy-ngs-utils
      > Could not resolve de.erichseifert.gral:gral-core:0.10.
         > Could not get resource 'http://mvn.erichseifert.de/maven2/de/erichseifert/gral/gral-core/0.10/gral-core-0.10.pom'.
            > Could not GET 'http://mvn.erichseifert.de/maven2/de/erichseifert/gral/gral-core/0.10/gral-core-0.10.pom'. Received status code 401 from server: Unauthorized

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

* Get more help at https://help.gradle.org

BUILD FAILED in 1m 15s

It seems like this is an issue with an external dependency but I was hoping that someone may know how to deal with it here?

[longqh3]

Hi, I checked the gral website in github (https://github.com/eseifert/gral). It said that, in order to Use Gral with Gradle, proper config should be changed like this.

dependencies {
    compile group: 'de.erichseifert.gral', name: 'gral-core', version: '0.11'
}

But I failed the following build process, so I just gave up since the gradle building was so annonying to debug......

[moldach]

I'm having the exact same issue on the following architecture:

$ cat /etc/os-release 
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

From what I understand ./gradle comes with bazam - how does one change the config for this?

I'm looking in the folder but I don't see any *.config files?

$ find . -name "*.config"

[moldach]

I also have another HPC with a different architecture which I can test:

CentOS8

$ ./gradlew clean jar
Downloading https://services.gradle.org/distributions/gradle-4.3.1-bin.zip
.....................................................................
Unzipping /home/moldach/.gradle/wrapper/dists/gradle-4.3.1-bin/7yzdu24db77gi3zukl2a7o0xx/gradle-4.3.1-bin.zip to /home/moldach/.gradle/wrapper/dists/gradle-4.3.1-bin/7yzdu24db77gi3zukl2a7o0xx
Set executable permissions for: /home/moldach/.gradle/wrapper/dists/gradle-4.3.1-bin/7yzdu24db77gi3zukl2a7o0xx/gradle-4.3.1/bin/gradle
Starting a Gradle Daemon (subsequent builds will be faster)
Download https://plugins.gradle.org/m2/gradle/plugin/com/github/maiflai/gradle-scalatest/0.15/gradle-scalatest-0.15.pom
Download https://plugins.gradle.org/m2/com/github/jengelman/gradle/plugins/shadow/1.2.3/shadow-1.2.3.pom
Download https://repo1.maven.org/maven2/org/apache/ant/ant/1.9.4/ant-1.9.4.pom
Download https://repo1.maven.org/maven2/org/ow2/asm/asm/5.0.3/asm-5.0.3.pom
Download https://repo1.maven.org/maven2/org/codehaus/plexus/plexus-utils/2.0.6/plexus-utils-2.0.6.pom
Download https://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.pom
Download https://repo1.maven.org/maven2/org/jdom/jdom2/2.0.5/jdom2-2.0.5.pom
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-commons/5.0.3/asm-commons-5.0.3.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-backports-compat23/2.4.4/groovy-backports-compat23-2.4.4.pom
Download https://repo1.maven.org/maven2/org/apache/ant/ant-parent/1.9.4/ant-parent-1.9.4.pom
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-parent/5.0.3/asm-parent-5.0.3.pom
Download https://repo1.maven.org/maven2/org/codehaus/plexus/plexus/2.0.7/plexus-2.0.7.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/25/commons-parent-25.pom
Download https://repo1.maven.org/maven2/org/ow2/ow2/1.3/ow2-1.3.pom
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-tree/5.0.3/asm-tree-5.0.3.pom
Download https://repo1.maven.org/maven2/org/apache/ant/ant-launcher/1.9.4/ant-launcher-1.9.4.pom
Download https://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.jar
Download https://repo1.maven.org/maven2/com/googlecode/javaewah/JavaEWAH/0.7.9/JavaEWAH-0.7.9.jar
Download https://plugins.gradle.org/m2/gradle/plugin/com/github/maiflai/gradle-scalatest/0.15/gradle-scalatest-0.15.jar
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-backports-compat23/2.4.4/groovy-backports-compat23-2.4.4.jar
Download https://plugins.gradle.org/m2/com/github/jengelman/gradle/plugins/shadow/1.2.3/shadow-1.2.3.jar
Download https://repo1.maven.org/maven2/org/ow2/asm/asm/5.0.3/asm-5.0.3.jar
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-tree/5.0.3/asm-tree-5.0.3.jar
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-commons/5.0.3/asm-commons-5.0.3.jar
Download https://repo1.maven.org/maven2/org/jdom/jdom2/2.0.5/jdom2-2.0.5.jar
Download https://repo1.maven.org/maven2/com/jcraft/jsch/0.1.53/jsch-0.1.53.jar
Download https://repo1.maven.org/maven2/org/eclipse/jdt/org.eclipse.jdt.annotation/1.1.0/org.eclipse.jdt.annotation-1.1.0.jar
Download https://repo1.maven.org/maven2/org/apache/ant/ant/1.9.4/ant-1.9.4.jar
Download https://repo1.maven.org/maven2/org/codehaus/plexus/plexus-utils/2.0.6/plexus-utils-2.0.6.jar
Download https://repo1.maven.org/maven2/org/apache/ant/ant-launcher/1.9.4/ant-launcher-1.9.4.jar
Download https://repo1.maven.org/maven2/org/eclipse/jgit/org.eclipse.jgit/4.1.1.201511131810-r/org.eclipse.jgit-4.1.1.201511131810-r.jar
Download https://repo1.maven.org/maven2/org/apache/commons/commons-math3/3.5/commons-math3-3.5.pom
Download https://repo1.maven.org/maven2/com/lowagie/itext/2.1.7/itext-2.1.7.pom
Download https://repo1.maven.org/maven2/commons-cli/commons-cli/1.1/commons-cli-1.1.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy/2.4.13/groovy-2.4.13.pom
Download https://repo1.maven.org/maven2/log4j/log4j/1.2.17/log4j-1.2.17.pom
Download https://repo1.maven.org/maven2/com/xlson/groovycsv/groovycsv/1.0/groovycsv-1.0.pom
Download https://repo1.maven.org/maven2/junit/junit/4.4/junit-4.4.pom
Download https://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.pom
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Download https://repo1.maven.org/maven2/org/apache/apache/7/apache-7.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/34/commons-parent-34.pom
Download https://repo1.maven.org/maven2/bouncycastle/bctsp-jdk14/138/bctsp-jdk14-138.pom
Download https://repo1.maven.org/maven2/bouncycastle/bcprov-jdk14/138/bcprov-jdk14-138.pom
Download https://repo1.maven.org/maven2/bouncycastle/bcmail-jdk14/138/bcmail-jdk14-138.pom
Download https://repo1.maven.org/maven2/net/sf/opencsv/opencsv/2.1/opencsv-2.1.pom
Download https://repo1.maven.org/maven2/org/bouncycastle/bctsp-jdk14/1.38/bctsp-jdk14-1.38.pom
Download https://repo1.maven.org/maven2/org/bouncycastle/bcprov-jdk14/1.38/bcprov-jdk14-1.38.pom
Download https://repo1.maven.org/maven2/org/bouncycastle/bcmail-jdk14/1.38/bcmail-jdk14-1.38.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-all/2.4.13/groovy-all-2.4.13.jar
Download https://repo1.maven.org/maven2/commons-cli/commons-cli/1.1/commons-cli-1.1.jar
Download https://repo1.maven.org/maven2/junit/junit/4.4/junit-4.4.jar
Download https://repo1.maven.org/maven2/org/bouncycastle/bctsp-jdk14/1.38/bctsp-jdk14-1.38.jar
Download https://repo1.maven.org/maven2/log4j/log4j/1.2.17/log4j-1.2.17.jar
Download https://repo1.maven.org/maven2/com/xlson/groovycsv/groovycsv/1.0/groovycsv-1.0.jar
Download https://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar
Download https://repo1.maven.org/maven2/org/apache/commons/commons-math3/3.5/commons-math3-3.5.jar
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy/2.4.13/groovy-2.4.13.jar
Download https://repo1.maven.org/maven2/net/sf/opencsv/opencsv/2.1/opencsv-2.1.jar
Download https://repo1.maven.org/maven2/com/lowagie/itext/2.1.7/itext-2.1.7.jar
Download https://repo1.maven.org/maven2/bouncycastle/bcmail-jdk14/138/bcmail-jdk14-138.jar
Download https://repo1.maven.org/maven2/org/bouncycastle/bcmail-jdk14/1.38/bcmail-jdk14-1.38.jar
Download https://repo1.maven.org/maven2/org/bouncycastle/bcprov-jdk14/1.38/bcprov-jdk14-1.38.jar
Download https://repo1.maven.org/maven2/bouncycastle/bcprov-jdk14/138/bcprov-jdk14-138.jar

> Configure project :groovy-ngs-utils:graxxia 
The Task.leftShift(Closure) method has been deprecated and is scheduled to be removed in Gradle 5.0. Please use Task.doLast(Action) instead.
        at build_5yevwiea03iyzhf1a3god8v0z.run(/work/mtgraovac_lab/tools/bazam/groovy-ngs-utils/graxxia/build.gradle:48)
        (Run with --stacktrace to get the full stack trace of this deprecation warning.)

Download https://repo1.maven.org/maven2/org/biojava/biojava-alignment/4.2.1/biojava-alignment-4.2.1.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-xml/2.4.13/groovy-xml-2.4.13.pom
Download https://repo1.maven.org/maven2/com/google/guava/guava/26.0-jre/guava-26.0-jre.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.pom
Download https://repo1.maven.org/maven2/org/yaml/snakeyaml/1.23/snakeyaml-1.23.pom
Download https://repo1.maven.org/maven2/commons-cli/commons-cli/1.4/commons-cli-1.4.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-math3/3.0/commons-math3-3.0.pom
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Download https://repo1.maven.org/maven2/org/codehaus/gpars/gpars/1.2.1/gpars-1.2.1.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-sql/2.4.13/groovy-sql-2.4.13.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-json/2.4.13/groovy-json-2.4.13.pom
Download https://repo1.maven.org/maven2/org/biojava/biojava-core/4.2.1/biojava-core-4.2.1.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-ant/2.4.13/groovy-ant-2.4.13.pom
Download https://repo1.maven.org/maven2/org/xerial/sqlite-jdbc/3.8.6/sqlite-jdbc-3.8.6.pom
Download https://repo1.maven.org/maven2/com/github/scribejava/scribejava/5.6.0/scribejava-5.6.0.pom
Download https://repo1.maven.org/maven2/org/biojava/biojava/4.2.1/biojava-4.2.1.pom
Download https://repo1.maven.org/maven2/com/google/guava/guava-parent/26.0-jre/guava-parent-26.0-jre.pom
Download https://repo1.maven.org/maven2/org/sonatype/oss/oss-parent/9/oss-parent-9.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/23/commons-parent-23.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/24/commons-parent-24.pom
Download https://repo1.maven.org/maven2/org/apache/ant/ant-junit/1.9.4/ant-junit-1.9.4.pom
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Download https://repo1.maven.org/maven2/org/apache/logging/log4j/log4j-core/2.5/log4j-core-2.5.pom
Download https://repo1.maven.org/maven2/org/apache/logging/log4j/log4j/2.5/log4j-2.5.pom
Download https://repo1.maven.org/maven2/org/biojava/biojava-phylo/4.2.1/biojava-phylo-4.2.1.pom
Download https://repo1.maven.org/maven2/org/biojava/thirdparty/forester/1.038/forester-1.038.pom
Download https://repo1.maven.org/maven2/org/tukaani/xz/1.0/xz-1.0.pom
Download https://repo1.maven.org/maven2/com/google/errorprone/error_prone_annotations/2.1.3/error_prone_annotations-2.1.3.pom
Download https://repo1.maven.org/maven2/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.pom
Download https://repo1.maven.org/maven2/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.pom
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Download https://repo1.maven.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.pom
Download https://repo1.maven.org/maven2/org/xerial/snappy/snappy-java/1.1.4/snappy-java-1.1.4.pom
Download https://repo1.maven.org/maven2/gov/nih/nlm/ncbi/ngs-java/1.2.4/ngs-java-1.2.4.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/5/commons-parent-5.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-templates/2.4.13/groovy-templates-2.4.13.pom
Download https://repo1.maven.org/maven2/commons-codec/commons-codec/1.5/commons-codec-1.5.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/20/commons-parent-20.pom
Download https://repo1.maven.org/maven2/org/tukaani/xz/1.5/xz-1.5.pom

FAILURE: Build failed with an exception.

* Where:
Build file '/work/mtgraovac_lab/tools/bazam/groovy-ngs-utils/build.gradle' line: 76

* What went wrong:
A problem occurred evaluating project ':groovy-ngs-utils'.
> Could not resolve all files for configuration ':groovy-ngs-utils:compile'.
   > Could not resolve de.erichseifert.gral:gral-core:0.10.
     Required by:
         project :groovy-ngs-utils
      > Could not resolve de.erichseifert.gral:gral-core:0.10.
         > Could not get resource 'http://mvn.erichseifert.de/maven2/de/erichseifert/gral/gral-core/0.10/gral-core-0.10.pom'.
            > Could not GET 'http://mvn.erichseifert.de/maven2/de/erichseifert/gral/gral-core/0.10/gral-core-0.10.pom'. Received status code 502 from server: Bad Gateway

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

* Get more help at https://help.gradle.org

BUILD FAILED in 38s

[moldach]

Also an issue building on Ubuntu 20.04.1:

$ cat /etc/os-release 
NAME="Ubuntu"
VERSION="20.04.1 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.1 LTS"
VERSION_ID="20.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=focal
UBUNTU_CODENAME=focal

$ git clone https://github.com/ssadedin/bazam.git && cd bazam && \
>      git submodule update --init --recursive && \
>      ./gradlew clean jar
Cloning into 'bazam'...
remote: Enumerating objects: 12, done.
remote: Counting objects: 100% (12/12), done.
remote: Compressing objects: 100% (9/9), done.
remote: Total 328 (delta 2), reused 9 (delta 1), pack-reused 316
Receiving objects: 100% (328/328), 1.57 MiB | 985.00 KiB/s, done.
Resolving deltas: 100% (110/110), done.
Submodule 'groovy-ngs-utils' (https://github.com/ssadedin/groovy-ngs-utils.git) registered for path 'groovy-ngs-utils'
Cloning into '/home/mtg/bin/bazam/groovy-ngs-utils'...
Submodule path 'groovy-ngs-utils': checked out 'a29c9c819d45448af637d4acf09351da677b3c9e'
Submodule 'graxxia' (https://github.com/ssadedin/graxxia.git) registered for path 'groovy-ngs-utils/graxxia'
Submodule 'htsjdk' (https://github.com/samtools/htsjdk.git) registered for path 'groovy-ngs-utils/htsjdk'
Cloning into '/home/mtg/bin/bazam/groovy-ngs-utils/graxxia'...
Cloning into '/home/mtg/bin/bazam/groovy-ngs-utils/htsjdk'...
Submodule path 'groovy-ngs-utils/graxxia': checked out 'a350316b8a4f07ea3bf52c54965ca11096674de9'
Submodule path 'groovy-ngs-utils/htsjdk': checked out 'adf428f970a73cfc467bcbc3eb6343a74abff7b5'
Downloading https://services.gradle.org/distributions/gradle-4.3.1-bin.zip
.....................................................................
Unzipping /home/mtg/.gradle/wrapper/dists/gradle-4.3.1-bin/7yzdu24db77gi3zukl2a7o0xx/gradle-4.3.1-bin.zip to /home/mtg/.gradle/wrapper/dists/gradle-4.3.1-bin/7yzdu24db77gi3zukl2a7o0xx
Set executable permissions for: /home/mtg/.gradle/wrapper/dists/gradle-4.3.1-bin/7yzdu24db77gi3zukl2a7o0xx/gradle-4.3.1/bin/gradle
Starting a Gradle Daemon (subsequent builds will be faster)
Download https://plugins.gradle.org/m2/gradle/plugin/com/palantir/gradle/gitversion/gradle-git-version/0.5.1/gradle-git-version-0.5.1.pom
Download https://plugins.gradle.org/m2/com/github/jengelman/gradle/plugins/shadow/1.2.3/shadow-1.2.3.pom
Download https://plugins.gradle.org/m2/gradle/plugin/com/github/maiflai/gradle-scalatest/0.15/gradle-scalatest-0.15.pom
Download https://repo1.maven.org/maven2/com/google/guava/guava/19.0/guava-19.0.pom
Download https://repo1.maven.org/maven2/org/eclipse/jgit/org.eclipse.jgit/4.1.1.201511131810-r/org.eclipse.jgit-4.1.1.201511131810-r.pom
Download https://repo1.maven.org/maven2/com/google/guava/guava-parent/19.0/guava-parent-19.0.pom
Download https://repo1.maven.org/maven2/org/eclipse/jgit/org.eclipse.jgit-parent/4.1.1.201511131810-r/org.eclipse.jgit-parent-4.1.1.201511131810-r.pom
Download https://repo1.maven.org/maven2/org/sonatype/oss/oss-parent/7/oss-parent-7.pom
Download https://repo1.maven.org/maven2/org/jdom/jdom2/2.0.5/jdom2-2.0.5.pom
Download https://repo1.maven.org/maven2/org/ow2/asm/asm/5.0.3/asm-5.0.3.pom
Download https://repo1.maven.org/maven2/org/apache/ant/ant/1.9.4/ant-1.9.4.pom
Download https://repo1.maven.org/maven2/org/apache/ant/ant-parent/1.9.4/ant-parent-1.9.4.pom
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-parent/5.0.3/asm-parent-5.0.3.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-backports-compat23/2.4.4/groovy-backports-compat23-2.4.4.pom
Download https://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.pom
Download https://repo1.maven.org/maven2/org/codehaus/plexus/plexus-utils/2.0.6/plexus-utils-2.0.6.pom
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-commons/5.0.3/asm-commons-5.0.3.pom
Download https://repo1.maven.org/maven2/org/ow2/ow2/1.3/ow2-1.3.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/25/commons-parent-25.pom
Download https://repo1.maven.org/maven2/org/codehaus/plexus/plexus/2.0.7/plexus-2.0.7.pom
Download https://repo1.maven.org/maven2/org/apache/apache/9/apache-9.pom
Download https://repo1.maven.org/maven2/com/googlecode/javaewah/JavaEWAH/0.7.9/JavaEWAH-0.7.9.pom
Download https://repo1.maven.org/maven2/com/jcraft/jsch/0.1.53/jsch-0.1.53.pom
Download https://repo1.maven.org/maven2/org/eclipse/jdt/org.eclipse.jdt.annotation/1.1.0/org.eclipse.jdt.annotation-1.1.0.pom
Download https://repo1.maven.org/maven2/org/slf4j/slf4j-api/1.7.2/slf4j-api-1.7.2.pom
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/httpclient/4.3.6/httpclient-4.3.6.pom
Download https://repo1.maven.org/maven2/org/sonatype/oss/oss-parent/5/oss-parent-5.pom
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/httpcomponents-client/4.3.6/httpcomponents-client-4.3.6.pom
Download https://repo1.maven.org/maven2/org/sonatype/oss/oss-parent/6/oss-parent-6.pom
Download https://repo1.maven.org/maven2/org/slf4j/slf4j-parent/1.7.2/slf4j-parent-1.7.2.pom
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/project/7/project-7.pom
Download https://repo1.maven.org/maven2/org/apache/apache/13/apache-13.pom
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-tree/5.0.3/asm-tree-5.0.3.pom
Download https://repo1.maven.org/maven2/org/apache/ant/ant-launcher/1.9.4/ant-launcher-1.9.4.pom
Download https://repo1.maven.org/maven2/commons-codec/commons-codec/1.6/commons-codec-1.6.pom
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/httpcore/4.3.3/httpcore-4.3.3.pom
Download https://repo1.maven.org/maven2/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.pom
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/httpcomponents-core/4.3.3/httpcomponents-core-4.3.3.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/22/commons-parent-22.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/28/commons-parent-28.pom
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-tree/5.0.3/asm-tree-5.0.3.jar
Download https://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.jar
Download https://repo1.maven.org/maven2/org/codehaus/plexus/plexus-utils/2.0.6/plexus-utils-2.0.6.jar
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-backports-compat23/2.4.4/groovy-backports-compat23-2.4.4.jar
Download https://repo1.maven.org/maven2/org/ow2/asm/asm/5.0.3/asm-5.0.3.jar
Download https://repo1.maven.org/maven2/com/google/guava/guava/19.0/guava-19.0.jar
Download https://repo1.maven.org/maven2/org/apache/ant/ant/1.9.4/ant-1.9.4.jar
Download https://repo1.maven.org/maven2/com/jcraft/jsch/0.1.53/jsch-0.1.53.jar
Download https://repo1.maven.org/maven2/com/googlecode/javaewah/JavaEWAH/0.7.9/JavaEWAH-0.7.9.jar
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/httpclient/4.3.6/httpclient-4.3.6.jar
Download https://repo1.maven.org/maven2/org/jdom/jdom2/2.0.5/jdom2-2.0.5.jar
Download https://repo1.maven.org/maven2/org/slf4j/slf4j-api/1.7.2/slf4j-api-1.7.2.jar
Download https://repo1.maven.org/maven2/org/eclipse/jgit/org.eclipse.jgit/4.1.1.201511131810-r/org.eclipse.jgit-4.1.1.201511131810-r.jar
Download https://repo1.maven.org/maven2/org/eclipse/jdt/org.eclipse.jdt.annotation/1.1.0/org.eclipse.jdt.annotation-1.1.0.jar
Download https://repo1.maven.org/maven2/org/apache/ant/ant-launcher/1.9.4/ant-launcher-1.9.4.jar
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/httpcore/4.3.3/httpcore-4.3.3.jar
Download https://repo1.maven.org/maven2/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
Download https://repo1.maven.org/maven2/commons-codec/commons-codec/1.6/commons-codec-1.6.jar
Download https://repo1.maven.org/maven2/org/ow2/asm/asm-commons/5.0.3/asm-commons-5.0.3.jar
Download https://plugins.gradle.org/m2/com/github/jengelman/gradle/plugins/shadow/1.2.3/shadow-1.2.3.jar
Download https://plugins.gradle.org/m2/gradle/plugin/com/palantir/gradle/gitversion/gradle-git-version/0.5.1/gradle-git-version-0.5.1.jar
Download https://plugins.gradle.org/m2/gradle/plugin/com/github/maiflai/gradle-scalatest/0.15/gradle-scalatest-0.15.jar
Download https://repo1.maven.org/maven2/org/apache/commons/commons-math3/3.5/commons-math3-3.5.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy/2.4.13/groovy-2.4.13.pom
Download https://repo1.maven.org/maven2/com/xlson/groovycsv/groovycsv/1.0/groovycsv-1.0.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-all/2.4.13/groovy-all-2.4.13.pom
Download https://repo1.maven.org/maven2/log4j/log4j/1.2.17/log4j-1.2.17.pom
Download https://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.pom
Download https://repo1.maven.org/maven2/commons-cli/commons-cli/1.1/commons-cli-1.1.pom
Download https://repo1.maven.org/maven2/com/lowagie/itext/2.1.7/itext-2.1.7.pom
Download https://repo1.maven.org/maven2/junit/junit/4.4/junit-4.4.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/34/commons-parent-34.pom
Download https://repo1.maven.org/maven2/org/apache/apache/7/apache-7.pom
Download https://repo1.maven.org/maven2/bouncycastle/bcprov-jdk14/138/bcprov-jdk14-138.pom
Download https://repo1.maven.org/maven2/bouncycastle/bctsp-jdk14/138/bctsp-jdk14-138.pom
Download https://repo1.maven.org/maven2/bouncycastle/bcmail-jdk14/138/bcmail-jdk14-138.pom
Download https://repo1.maven.org/maven2/net/sf/opencsv/opencsv/2.1/opencsv-2.1.pom
Download https://repo1.maven.org/maven2/org/bouncycastle/bctsp-jdk14/1.38/bctsp-jdk14-1.38.pom
Download https://repo1.maven.org/maven2/org/bouncycastle/bcmail-jdk14/1.38/bcmail-jdk14-1.38.pom
Download https://repo1.maven.org/maven2/org/bouncycastle/bcprov-jdk14/1.38/bcprov-jdk14-1.38.pom
Download https://repo1.maven.org/maven2/junit/junit/4.4/junit-4.4.jar
Download https://repo1.maven.org/maven2/com/xlson/groovycsv/groovycsv/1.0/groovycsv-1.0.jar
Download https://repo1.maven.org/maven2/log4j/log4j/1.2.17/log4j-1.2.17.jar
Download https://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar
Download https://repo1.maven.org/maven2/com/lowagie/itext/2.1.7/itext-2.1.7.jar
Download https://repo1.maven.org/maven2/bouncycastle/bcmail-jdk14/138/bcmail-jdk14-138.jar
Download https://repo1.maven.org/maven2/net/sf/opencsv/opencsv/2.1/opencsv-2.1.jar
Download https://repo1.maven.org/maven2/commons-cli/commons-cli/1.1/commons-cli-1.1.jar
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy/2.4.13/groovy-2.4.13.jar
Download https://repo1.maven.org/maven2/org/bouncycastle/bcmail-jdk14/1.38/bcmail-jdk14-1.38.jar
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-all/2.4.13/groovy-all-2.4.13.jar
Download https://repo1.maven.org/maven2/org/apache/commons/commons-math3/3.5/commons-math3-3.5.jar
Download https://repo1.maven.org/maven2/org/bouncycastle/bcprov-jdk14/1.38/bcprov-jdk14-1.38.jar
Download https://repo1.maven.org/maven2/bouncycastle/bcprov-jdk14/138/bcprov-jdk14-138.jar
Download https://repo1.maven.org/maven2/org/bouncycastle/bctsp-jdk14/1.38/bctsp-jdk14-1.38.jar

> Configure project :groovy-ngs-utils:graxxia 
The Task.leftShift(Closure) method has been deprecated and is scheduled to be removed in Gradle 5.0. Please use Task.doLast(Action) instead.
        at build_do2ji8bfdeqqguv1th5jrp519.run(/home/mtg/bin/bazam/groovy-ngs-utils/graxxia/build.gradle:48)
        (Run with --stacktrace to get the full stack trace of this deprecation warning.)

Download https://repo1.maven.org/maven2/org/apache/commons/commons-math3/3.0/commons-math3-3.0.pom
Download https://repo1.maven.org/maven2/org/yaml/snakeyaml/1.23/snakeyaml-1.23.pom
Download https://repo1.maven.org/maven2/org/biojava/biojava-alignment/4.2.1/biojava-alignment-4.2.1.pom
Download https://repo1.maven.org/maven2/org/biojava/biojava-core/4.2.1/biojava-core-4.2.1.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-ant/2.4.13/groovy-ant-2.4.13.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-sql/2.4.13/groovy-sql-2.4.13.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.pom
Download https://repo1.maven.org/maven2/com/github/scribejava/scribejava-core/5.6.0/scribejava-core-5.6.0.pom
Download https://repo1.maven.org/maven2/org/codehaus/gpars/gpars/1.2.1/gpars-1.2.1.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-json/2.4.13/groovy-json-2.4.13.pom
Download https://repo1.maven.org/maven2/com/google/guava/guava/26.0-jre/guava-26.0-jre.pom
Download https://repo1.maven.org/maven2/org/biojava/biojava/4.2.1/biojava-4.2.1.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/23/commons-parent-23.pom
Download https://repo1.maven.org/maven2/commons-cli/commons-cli/1.4/commons-cli-1.4.pom
Download https://repo1.maven.org/maven2/org/xerial/sqlite-jdbc/3.8.6/sqlite-jdbc-3.8.6.pom
Download https://repo1.maven.org/maven2/com/google/guava/guava-parent/26.0-jre/guava-parent-26.0-jre.pom
Download https://repo1.maven.org/maven2/com/github/scribejava/scribejava/5.6.0/scribejava-5.6.0.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/24/commons-parent-24.pom
Download https://repo1.maven.org/maven2/org/sonatype/oss/oss-parent/9/oss-parent-9.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/42/commons-parent-42.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-xml/2.4.13/groovy-xml-2.4.13.pom
Download https://repo1.maven.org/maven2/org/apache/apache/18/apache-18.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-groovydoc/2.4.13/groovy-groovydoc-2.4.13.pom
Download https://repo1.maven.org/maven2/org/apache/ant/ant-antlr/1.9.4/ant-antlr-1.9.4.pom
Download https://repo1.maven.org/maven2/org/apache/ant/ant-junit/1.9.4/ant-junit-1.9.4.pom
Download https://repo1.maven.org/maven2/org/multiverse/multiverse-core/0.7.0/multiverse-core-0.7.0.pom
Download https://repo1.maven.org/maven2/org/codehaus/jsr166-mirror/jsr166y/1.7.0/jsr166y-1.7.0.pom
Download https://repo1.maven.org/maven2/org/multiverse/multiverse/0.7.0/multiverse-0.7.0.pom
Download https://repo1.maven.org/maven2/org/apache/logging/log4j/log4j-api/2.5/log4j-api-2.5.pom
Download https://repo1.maven.org/maven2/org/apache/logging/log4j/log4j-core/2.5/log4j-core-2.5.pom
Download https://repo1.maven.org/maven2/org/slf4j/slf4j-api/1.7.14/slf4j-api-1.7.14.pom
Download https://repo1.maven.org/maven2/org/apache/logging/log4j/log4j-slf4j-impl/2.5/log4j-slf4j-impl-2.5.pom
Download https://repo1.maven.org/maven2/org/slf4j/slf4j-parent/1.7.14/slf4j-parent-1.7.14.pom
Download https://repo1.maven.org/maven2/org/apache/logging/log4j/log4j/2.5/log4j-2.5.pom
Download https://repo1.maven.org/maven2/org/biojava/biojava-phylo/4.2.1/biojava-phylo-4.2.1.pom
Download https://repo1.maven.org/maven2/org/biojava/thirdparty/forester/1.038/forester-1.038.pom
Download https://repo1.maven.org/maven2/org/tukaani/xz/1.0/xz-1.0.pom
Download https://repo1.maven.org/maven2/com/google/code/findbugs/jsr305/3.0.2/jsr305-3.0.2.pom
Download https://repo1.maven.org/maven2/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.pom
Download https://repo1.maven.org/maven2/com/google/errorprone/error_prone_annotations/2.1.3/error_prone_annotations-2.1.3.pom
Download https://repo1.maven.org/maven2/org/codehaus/mojo/animal-sniffer-annotations/1.14/animal-sniffer-annotations-1.14.pom
Download https://repo1.maven.org/maven2/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.pom
Download https://repo1.maven.org/maven2/com/google/errorprone/error_prone_parent/2.1.3/error_prone_parent-2.1.3.pom
Download https://repo1.maven.org/maven2/org/codehaus/mojo/animal-sniffer-parent/1.14/animal-sniffer-parent-1.14.pom
Download https://repo1.maven.org/maven2/org/codehaus/mojo/mojo-parent/34/mojo-parent-34.pom
Download https://repo1.maven.org/maven2/org/codehaus/codehaus-parent/4/codehaus-parent-4.pom
Download https://repo1.maven.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.pom
Download https://repo1.maven.org/maven2/org/xerial/snappy/snappy-java/1.1.4/snappy-java-1.1.4.pom
Download https://repo1.maven.org/maven2/gov/nih/nlm/ncbi/ngs-java/1.2.4/ngs-java-1.2.4.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/5/commons-parent-5.pom
Download https://repo1.maven.org/maven2/org/apache/apache/4/apache-4.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/groovy-templates/2.4.13/groovy-templates-2.4.13.pom
Download https://repo1.maven.org/maven2/commons-codec/commons-codec/1.5/commons-codec-1.5.pom
Download https://repo1.maven.org/maven2/org/apache/commons/commons-parent/20/commons-parent-20.pom
Download https://repo1.maven.org/maven2/org/tukaani/xz/1.5/xz-1.5.pom

FAILURE: Build failed with an exception.

* Where:
Build file '/home/mtg/bin/bazam/groovy-ngs-utils/build.gradle' line: 76

* What went wrong:
A problem occurred evaluating project ':groovy-ngs-utils'.
> Could not resolve all files for configuration ':groovy-ngs-utils:compile'.
   > Could not resolve de.erichseifert.gral:gral-core:0.10.
     Required by:
         project :groovy-ngs-utils
      > Could not resolve de.erichseifert.gral:gral-core:0.10.
         > Could not get resource 'http://mvn.erichseifert.de/maven2/de/erichseifert/gral/gral-core/0.10/gral-core-0.10.pom'.
            > Could not GET 'http://mvn.erichseifert.de/maven2/de/erichseifert/gral/gral-core/0.10/gral-core-0.10.pom'. Received status code 502 from server: Bad Gateway

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

* Get more help at https://help.gradle.org

BUILD FAILED in 27s

[drmrgd]

I am also having the same problem as others getting this to build. Is there, by chance, any update to this issue or any suggestion as to how to get it to build?

[ManavalanG]

Ran in to this issue and then found that bazam can be installed using conda. Of course, this will work only with the released versions (currently 1.0.1 released in oct 2018).