cannot compile htsjdk-2.4.1 on Cygwin on windows

arjunvadapalli commented 8 years ago

Subject of the issue

Downloaded htsjdk-2.4.1, unzipped file and ran gradlew script on Cygwin prompt. The necessary plugins were downloaded but the compilation ended with an error saying

FAILURE: Build failed with an exception.

Where: Build file 'C:\Progs\htsjdk-2.4.1\build.gradle' line: 61
What went wrong: A problem occurred evaluating root project 'htsjdk-2.4.1'.

Cannot find '.git' directory

Your environment
version of htsjdk - 2.4.1
version of java - 1.8.0_91
which OS - windows 7
Steps to reproduce

Tell us how to reproduce this issue. If possible, include a short code snippet to demonstrate the problem.

Expected behaviour

compile htsjdk.jar

Actual behaviour

Tell us what happens instead

arjunvadapalli commented 8 years ago

There is .github directory but no .git directory.

droazen commented 8 years ago

To build htsjdk from source, you first need to clone the htsjdk github repository using the "git clone" command, and then run gradle within your clone.

mmokrejs commented 8 years ago

Quoting from #660:

Failing to build if the .git directory isn't found is a known issue ( #636 ). We thought it was very low priority, but it's an easy fix so if it's causing problems we can definitely address that.

So, why does this happen if I start from https://github.com/samtools/htsjdk/archive/htsjdk-2.5.1.tar.gz file?

>>> Emerging (26 of 101) dev-java/htsjdk-2.5.1::science
 * htsjdk-2.5.1.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ...                                                                                                                                                                                                                                                             [ ok ]
 * Using: oracle-jdk-bin-1.8
>>> Unpacking source...
>>> Unpacking htsjdk-2.5.1.tar.gz to /scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work
>>> Source unpacked in /scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work
>>> Preparing source in /scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work/htsjdk-2.5.1 ...
>>> Source prepared.
>>> Configuring source in /scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work/htsjdk-2.5.1 ...
Rewriting attributes
Rewriting ./build.xml
>>> Source configured.
>>> Compiling source in /scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work/htsjdk-2.5.1 ...
Downloading https://services.gradle.org/distributions/gradle-2.13-bin.zip
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Unzipping /scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work/wrapper/dists/gradle-2.13-bin/4xsgxlfjcxvrea7akf941nvc7/gradle-2.13-bin.zip to /scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work/wrapper/dists/gradle-2.13-bin/4xsgxlfjcxvrea7akf941nvc7
Set executable permissions for: /scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work/wrapper/dists/gradle-2.13-bin/4xsgxlfjcxvrea7akf941nvc7/gradle-2.13/bin/gradle
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://repo1.maven.org/maven2/org/kt3k/gradle/plugin/coveralls-gradle-plugin/2.6.3/coveralls-gradle-plugin-2.6.3.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/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/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/ow2/asm/asm-parent/5.0.3/asm-parent-5.0.3.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/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/codehaus/groovy/groovy-backports-compat23/2.4.4/groovy-backports-compat23-2.4.4.pom
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/httpmime/4.3/httpmime-4.3.pom
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/httpcomponents-client/4.3/httpcomponents-client-4.3.pom
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/project/7/project-7.pom
Download https://repo1.maven.org/maven2/org/codehaus/groovy/modules/http-builder/http-builder/0.7.1/http-builder-0.7.1.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/org/apache/httpcomponents/httpclient/4.3/httpclient-4.3.pom
Download https://repo1.maven.org/maven2/net/sf/json-lib/json-lib/2.3/json-lib-2.3.pom
Download https://repo1.maven.org/maven2/net/sourceforge/nekohtml/nekohtml/1.9.16/nekohtml-1.9.16.pom
Download https://repo1.maven.org/maven2/xml-resolver/xml-resolver/1.2/xml-resolver-1.2.pom
Download https://repo1.maven.org/maven2/commons-beanutils/commons-beanutils/1.8.0/commons-beanutils-1.8.0.pom
Download https://repo1.maven.org/maven2/net/sf/ezmorph/ezmorph/1.0.6/ezmorph-1.0.6.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/sonatype/oss/oss-parent/6/oss-parent-6.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/org/slf4j/slf4j-api/1.7.2/slf4j-api-1.7.2.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/eclipse/jdt/org.eclipse.jdt.annotation/1.1.0/org.eclipse.jdt.annotation-1.1.0.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/apache/httpcomponents/httpcomponents-client/4.3.6/httpcomponents-client-4.3.6.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/org/apache/httpcomponents/httpcomponents-core/4.3.3/httpcomponents-core-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://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/com/github/jengelman/gradle/plugins/shadow/1.2.3/shadow-1.2.3.jar
Download https://repo1.maven.org/maven2/org/kt3k/gradle/plugin/coveralls-gradle-plugin/2.6.3/coveralls-gradle-plugin-2.6.3.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/jdom/jdom2/2.0.5/jdom2-2.0.5.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-commons/5.0.3/asm-commons-5.0.3.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/groovy/groovy-backports-compat23/2.4.4/groovy-backports-compat23-2.4.4.jar
Download https://repo1.maven.org/maven2/org/apache/httpcomponents/httpmime/4.3/httpmime-4.3.jar
Download https://repo1.maven.org/maven2/org/codehaus/groovy/modules/http-builder/http-builder/0.7.1/http-builder-0.7.1.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/apache/ant/ant-launcher/1.9.4/ant-launcher-1.9.4.jar
Download https://repo1.maven.org/maven2/net/sf/json-lib/json-lib/2.3/json-lib-2.3-jdk15.jar
Download https://repo1.maven.org/maven2/net/sourceforge/nekohtml/nekohtml/1.9.16/nekohtml-1.9.16.jar
Download https://repo1.maven.org/maven2/xml-resolver/xml-resolver/1.2/xml-resolver-1.2.jar
Download https://repo1.maven.org/maven2/commons-beanutils/commons-beanutils/1.8.0/commons-beanutils-1.8.0.jar
Download https://repo1.maven.org/maven2/net/sf/ezmorph/ezmorph/1.0.6/ezmorph-1.0.6.jar
Download https://repo1.maven.org/maven2/xerces/xercesImpl/2.9.1/xercesImpl-2.9.1.jar
Download https://repo1.maven.org/maven2/xml-apis/xml-apis/1.3.04/xml-apis-1.3.04.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/slf4j/slf4j-api/1.7.2/slf4j-api-1.7.2.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/httpcomponents/httpclient/4.3.6/httpclient-4.3.6.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

FAILURE: Build failed with an exception.

* Where:
Build file '/scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work/htsjdk-2.5.1/build.gradle' line: 52

* What went wrong:
A problem occurred evaluating root project 'htsjdk-2.5.1'.
> Cannot find '.git' directory

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

BUILD FAILED

Total time: 36.403 secs
 * ERROR: dev-java/htsjdk-2.5.1::science failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line 133:  Called src_compile
 *   environment, line 4036:  Called die
 * The specific snippet of code:
 *       GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
 * 
 * If you need support, post the output of `emerge --info '=dev-java/htsjdk-2.5.1::science'`,
 * the complete build log and the output of `emerge -pqv '=dev-java/htsjdk-2.5.1::science'`.
!!! When you file a bug report, please include the following information:
GENTOO_VM=oracle-jdk-bin-1.8  CLASSPATH="" JAVA_HOME="/opt/oracle-jdk-bin-1.8.0.92"
JAVACFLAGS="-source 1.8 -target 1.8" COMPILER=""
and of course, the output of emerge --info =htsjdk-2.5.1
 * The complete build log is located at '/scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/temp/build.log'.
 * The ebuild environment file is located at '/scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/temp/environment'.
 * Working directory: '/scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work/htsjdk-2.5.1'
 * S: '/scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/work/htsjdk-2.5.1'

>>> Failed to emerge dev-java/htsjdk-2.5.1, Log file:

>>>  '/scratch/var/tmp/portage/dev-java/htsjdk-2.5.1/temp/build.log'

droazen commented 8 years ago

@mmokrejs Because that .tar.gz archive contains the code from this repository, but is not itself a git repository. You need to git clone this repository, and build within that clone.

mmokrejs commented 8 years ago

Do you mean this?

gzip -dc htsjdk-2.5.1.tar.gz | tar xf -
cd htsjdk-2.5.1
git clone https://github.com/samtools/htsjdk.git
./gradlew

Or should I fiddle with $GIT_DIR or $GIT_WORK_TREE or $GIT_COMMON_DIR env variables? Note I have no write access to $HOME/.git from under this user, so I need to eventually redirect git to store its crap in some temp space. Ideally in current working directory.

droazen commented 8 years ago

You don't need to download the .tar.gz at all. Just git clone this repository, cd into the clone, and run ./gradlew jar to build an htsjdk-only jar, or ./gradlew shadowJar to build a monolithic jar that includes htsjdk plus all of htsjdk's dependencies. See the README for this repo for more build options.

samtools / htsjdk