diff --git a/Dockerfile b/Dockerfile index 29626ec..bcc4606 100644 --- a/Dockerfile +++ b/Dockerfile @@ -69,11 +69,13 @@ ENV PATH /opt/gradle/bin:${PATH} COPY bin /tmp/xenocp/bin COPY src /tmp/xenocp/src COPY dependencies /tmp/xenocp/dependencies +COPY gradle /tmp/xenocp/gradle +COPY gradlew /tmp/xenocp/gradlew COPY build.gradle /tmp/xenocp/build.gradle COPY settings.gradle /tmp/xenocp/settings.gradle RUN cd /tmp/xenocp \ - && gradle installDist \ + && ./gradlew installDist \ && cp -r build/install/xenocp /opt FROM ubuntu:20.04 diff --git a/README.md b/README.md index 94b3c11..6c28d83 100755 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ XenoCP can be easily incorporated into any workflow, as it takes a BAM file as input and efficiently cleans up the mouse contamination. The output is a clean human BAM file that could be used for downstream genomic analysis. -## Getting started +## Quick Start XenoCP can be run in the cloud on DNAnexus at https://platform.dnanexus.com/app/stjude_xenocp @@ -39,7 +39,38 @@ XenoCP workflow: -## Prerequisites +## Reference Files + +XenoCP performs mapping against the host genome, so it requires indexes for the +host reference genome and mapper being used. + +A common use case is cleansing DNA reads with a mouse host. For this use case, +you can download the a BWA index for MGSCv37 from +http://ftp.stjude.org/pub/software/xenocp/reference/MGSCv37 + +To build your own reference files, first download the FASTA file for your genome +assembly. Then, create the index for your mapper: + +### BWA for DNA Reads + +``` +$ bwa index -p $FASTA $FASTA +``` + +### STAR for RNA Reads + +Download an annotation file such as gencode, and then run: + +``` +$ STAR --runMode genomeGenerate --genomeDir STAR --genomeFastaFiles $FASTA --sjdbGTFfile $ANNOTATION --sjdbOverhang 125 +``` + +## Local Usage without Docker + +### Prerequisites + +First, install the following prerequisites. Note that if you are only using one +of the two mappers, bwa and STAR, you can omit the other. * [bwa] =0.7.13 * [STAR] =2.7.1a @@ -73,28 +104,25 @@ disabled. [zlib]: https://www.zlib.net/ [sambamba]: http://lomereiter.github.io/sambamba/ +### Obtain and Build XenoCP - -## Local usage - - -### Obtain XenoCP - -Clone XenoCP from GitHub: +Clone XenoCP from GitHub: ``` git clone https://github.com/stjude/XenoCP.git ``` -### Build XenoCP - -Once the prerequisites are satisfied, build XenoCP using Gradle. +Build XenoCP using Gradle: ``` $ gradle installDist ``` -Add the artifacts under `build/install/xenocp/lib` to your Java `CLASSPATH`. -Add the artifacts under `build/install/xenocp/bin` to your `PATH`. +Add the artifacts under `build/install/xenocp` to your `PATH` and your Java `CLASSPATH`: + +``` +export PATH=$PATH:`pwd`/build/install/xenocp/bin +export CLASSPATH=$CLASSPATH:`pwd`/build/install/xenocp/lib/* +``` ### Inputs @@ -134,25 +162,8 @@ output_prefix: xenocp- output_extension: bam ``` -### Create Reference Files - -Download the FASTA file for your genome assembly and run the following commands to create other files: -#### BWA reference files -``` -$ bwa index -p $FASTA $FASTA -``` -#### STAR reference files -In addition the genomic FASTA, STAR reference should use an annotation file (e.g. gencode). -``` -$ STAR --runMode genomeGenerate --genomeDir STAR --genomeFastaFiles $FASTA --sjdbGTFfile $ANNOTATION --sjdbOverhang 125 -``` - [CWL inputs]: https://www.commonwl.org/user_guide/02-1st-example/index.html -### Download MGSCv37 reference files - -Reference files are provided for version MGSCv37 of mouse and are available from http://ftp.stjude.org/pub/software/xenocp/reference/MGSCv37 - ### Run XenoCP uses [CWL] to describe its workflow. @@ -162,12 +173,12 @@ Then run the following. ``` $ mkdir results -$ cwltool --outdir results cwl/xenocp.cwl sample_data/input_data/inputs_local.yml +$ cwltool --preserve-environment CLASSPATH --no-container --outdir results cwl/xenocp.cwl sample_data/input_data/inputs_local.yml ``` [CWL]: https://www.commonwl.org/ -## Docker +## Local Usage with Docker XenoCP provides a [Dockerfile] that builds an image with all the included dependencies. To use this image, install [Docker] for your platform. @@ -216,6 +227,11 @@ $ docker run \ /data/inputs.yml ``` +Note: when running using Singularity on an HPC, problems can arise if the +default temporary file location, /tmp, is small. To solve this, include +`-W ` when executing via Singularity to redirect temp files to a +larger directory ``. + [Dockerfile]: ./Dockerfile ## Evaluate test data results diff --git a/bin/java.sh b/bin/java.sh index 769e542..095d2b0 100755 --- a/bin/java.sh +++ b/bin/java.sh @@ -1,5 +1,10 @@ #!/usr/bin/env bash +# If the classpath is already set, then delegate directly to java +if [ "$CLASSPATH" != "" ]; then exec java "$@"; fi + +# Otherwise, build an appropriate classpath +# This section assumes you are running inside the container for arg in "$@"; do case $arg in org.stjude.compbio.*) diff --git a/bin/picard b/bin/picard index fea6036..460346a 100755 --- a/bin/picard +++ b/bin/picard @@ -1,2 +1,8 @@ #!/usr/bin/env bash + +# If the classpath is already set, then invoke PicardCommandLine, allowing +# java to use the classpath. +if [ "$CLASSPATH" != "" ]; then exec java picard.cmdline.PicardCommandLine "$@"; fi + +# Otherwise, use the full picard jar; this assumes you're running in the container. java -jar /opt/picard/lib/picard*.jar "$@" diff --git a/build.gradle b/build.gradle index 2339503..d3a2359 100644 --- a/build.gradle +++ b/build.gradle @@ -20,24 +20,24 @@ distributions { // Puts the compiled xenocp jar into lib from jar // Puts all of the compile dependencies into lib - from configurations.compile + from configurations.compileClasspath } } } } repositories { - jcenter() + mavenCentral() } dependencies { - compile 'com.github.broadinstitute:picard:2.6.0' - compile 'commons-cli:commons-cli:1.2' - compile 'com.github.samtools:htsjdk:2.19.0' + implementation 'com.github.broadinstitute:picard:2.19.2' + implementation 'commons-cli:commons-cli:1.2' + implementation 'com.github.samtools:htsjdk:2.19.0' - compile files('dependencies/lib/java/xenocp-dependencies.jar') + implementation files('dependencies/lib/java/xenocp-dependencies.jar') - testCompile 'junit:junit:4.10' + testImplementation 'junit:junit:4.10' } group = 'org.stjude.compbio.xenocp' diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 0000000..7454180 Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 0000000..ffed3a2 --- /dev/null +++ b/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,5 @@ +distributionBase=GRADLE_USER_HOME +distributionPath=wrapper/dists +distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip +zipStoreBase=GRADLE_USER_HOME +zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew new file mode 100755 index 0000000..1b6c787 --- /dev/null +++ b/gradlew @@ -0,0 +1,234 @@ +#!/bin/sh + +# +# Copyright © 2015-2021 the original authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +############################################################################## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# +############################################################################## + +# Attempt to set APP_HOME + +# Resolve links: $0 may be a link +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac +done + +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit + +APP_NAME="Gradle" +APP_BASE_NAME=${0##*/} + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD=maximum + +warn () { + echo "$*" +} >&2 + +die () { + echo + echo "$*" + echo + exit 1 +} >&2 + +# OS specific support (must be 'true' or 'false'). +cygwin=false +msys=false +darwin=false +nonstop=false +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; +esac + +CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar + + +# Determine the Java command to use to start the JVM. +if [ -n "$JAVA_HOME" ] ; then + if [ -x "$JAVA_HOME/jre/sh/java" ] ; then + # IBM's JDK on AIX uses strange locations for the executables + JAVACMD=$JAVA_HOME/jre/sh/java + else + JAVACMD=$JAVA_HOME/bin/java + fi + if [ ! -x "$JAVACMD" ] ; then + die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +else + JAVACMD=java + which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." +fi + +# Increase the maximum file descriptors if we can. +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac +fi + +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. + +# For Cygwin or MSYS, switch paths to Windows format before running java +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) + + # Now convert the arguments - kludge to limit ourselves to /bin/sh + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) + fi + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg + done +fi + +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# + +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' + +exec "$JAVACMD" "$@" diff --git a/gradlew.bat b/gradlew.bat new file mode 100644 index 0000000..ac1b06f --- /dev/null +++ b/gradlew.bat @@ -0,0 +1,89 @@ +@rem +@rem Copyright 2015 the original author or authors. +@rem +@rem Licensed under the Apache License, Version 2.0 (the "License"); +@rem you may not use this file except in compliance with the License. +@rem You may obtain a copy of the License at +@rem +@rem https://www.apache.org/licenses/LICENSE-2.0 +@rem +@rem Unless required by applicable law or agreed to in writing, software +@rem distributed under the License is distributed on an "AS IS" BASIS, +@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +@rem See the License for the specific language governing permissions and +@rem limitations under the License. +@rem + +@if "%DEBUG%" == "" @echo off +@rem ########################################################################## +@rem +@rem Gradle startup script for Windows +@rem +@rem ########################################################################## + +@rem Set local scope for the variables with windows NT shell +if "%OS%"=="Windows_NT" setlocal + +set DIRNAME=%~dp0 +if "%DIRNAME%" == "" set DIRNAME=. +set APP_BASE_NAME=%~n0 +set APP_HOME=%DIRNAME% + +@rem Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + +@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" + +@rem Find java.exe +if defined JAVA_HOME goto findJavaFromJavaHome + +set JAVA_EXE=java.exe +%JAVA_EXE% -version >NUL 2>&1 +if "%ERRORLEVEL%" == "0" goto execute + +echo. +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:findJavaFromJavaHome +set JAVA_HOME=%JAVA_HOME:"=% +set JAVA_EXE=%JAVA_HOME%/bin/java.exe + +if exist "%JAVA_EXE%" goto execute + +echo. +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:execute +@rem Setup the command line + +set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + + +@rem Execute Gradle +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %* + +:end +@rem End local scope for the variables with windows NT shell +if "%ERRORLEVEL%"=="0" goto mainEnd + +:fail +rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of +rem the _cmd.exe /c_ return code! +if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 +exit /b 1 + +:mainEnd +if "%OS%"=="Windows_NT" endlocal + +:omega