Merge branch 'release/v1.5'

milaboratory · Jun 7, 2017 · 00cd925 · 00cd925
2 parents dceb5a8 + f055a8b
commit 00cd925
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Showing 8 changed files with 354 additions and 63 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,18 @@
+language: java
+
+sudo: false
+
+git:
+  submodules: false
+
+before_install:
+  - sed -i 's/[email protected]:/https:\/\/github.com\//' .gitmodules
+  - git submodule update --init --recursive
+  - cd milib && mvn clean install -DskipTests -B && cd ..
+
+jdk:
+  - openjdk7
+
+cache:
+  directories:
+  - $HOME/.m2
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,11 @@
 
+MiTools 1.5 ( 7 Jun 2017)
+========================
+
+-- Memory-efficient `randomize` action for single-end and paired-end fastq files
+-- Build host information now is saved to resulting binary artefact
+
+
 MiTools 1.4 (14 Jul 2016)
 ========================
 

diff --git a/README.md b/README.md
@@ -3,9 +3,68 @@ MiTools
 
 MiTools: yet another Next Generation Sequencing (NGS) data processing tool (based on MiLib)
 
+## Installation / Download
+
+#### Using Homebrew on Mac OS X or Linux ([linuxbrew](http://linuxbrew.sh/))
+
+    brew tap milaboratory/all
+    brew install mitools
+
+or just
+
+    brew install milaboratory/all/mitools
+
+to upgrade already installed MiTools to the newest version:
+
+    brew update
+    brew upgrade mitools
+
+#### Manual install (any OS)
+
+* download latest MiTools version from [release page](https://github.com/milaboratory/mitools/releases/latest)
+* unzip the archive
+* add resulting folder to your ``PATH`` variable
+  * or add symbolic link for ``mitools`` script to your ``bin`` folder
+  * or use MiTools directly by specifying full path to the executable script
+
+#### Requirements
+
+* Any OS with Java support (Linux, Windows, Mac OS X, etc..)
+* Java 1.7 or higher
+
+## Usage
+
+Cutting input fastq file to specified read length:
+
+    mitools cut -l 50 input.fastq.gz output.fastq.gz
+
+Reverse-complement all reads:
+
+    mitools rc input.fastq.gz output.fastq.gz
+
+Merge-overlap paired-end reads (like PEAR but works better in our experience; fast - based on [bitap](https://en.wikipedia.org/wiki/Bitap_algorithm) algorithm):
+
+    mitools merge input_R1.fastq.gz input_R2.fastq.gz output.fastq.gz
+
+Split input file into chunks of 1M reads:
+
+    mitools split -c 1000000 input.fastq.gz output_{P}.fastq.gz
+
+will produce ```output_0.fastq.gz, output_1.fastq.gz, ...``` files.
+
+See ```mitools -h``` for available command paramenters and other useful actions.
+
+## Documentation
+
+See output of
+
+    mitools -h
+
+for available actions.
+
 ## License
 
-   Copyright 2015 MiLaboratory.com
+   Copyright 2016 MiLaboratory.com
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

diff --git a/milib b/milib
diff --git a/mitools b/mitools
@@ -48,10 +48,17 @@ case $os in
         dir=$(dirname "$(readlinkUniversal "$0")")
     ;;
     Linux)
-        rFreeMb=$(free -m | head -n 3 | tail -n 1 | awk '{ print $4 }')
+        rFreeMb=$(free -m | grep Mem | awk '{ print $4 }')
         maxMb=$(($rFreeMb-$delta))
         dir="$(dirname "$(readlink -f "$0")")"
     ;;
+    FreeBSD)
+        freeBlocks=$(vmstat -s | grep -E 'free$' | awk '{ print $1 }')
+        inactiveBlocks=$(vmstat -s | grep inactive | awk '{ print $1 }')
+        freeMb=$(( ($freeBlocks+$inactiveBlocks)*4096/1048576 ))
+        maxMb=$(($freeMb-$delta))
+        dir=$(dirname "$(readlinkUniversal "$0")")    
+    ;;
     *)
        echo "Unknown OS."
        exit 1
@@ -143,4 +150,4 @@ then
     exit 1
 fi
 
-$java -Dapp.path=$dir -Dapp.command=mixcr -XX:+AggressiveOpts "${javaArgs[@]}" -jar $jar "${appArgs[@]}"
+$java -Dapp.path=$dir -Dapp.command=mitools -XX:+AggressiveOpts "${javaArgs[@]}" -jar $jar "${appArgs[@]}"
diff --git a/pom.xml b/pom.xml
@@ -19,7 +19,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mitools</artifactId>
-    <version>1.4</version>
+    <version>1.5</version>
     <packaging>jar</packaging>
     <name>MiTools</name>
     <url>https://github.com/milaboratory/mitools</url>
@@ -31,6 +31,11 @@
         <relativePath/>
     </parent>
 
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <milib.version>1.8</milib.version>
+    </properties>
+
     <description>
         Yet another Java library for Next Generation Sequencing (NGS) data processing.
     </description>
@@ -43,6 +48,38 @@
         </license>
     </licenses>
 
+    <dependencies>
+        <dependency>
+            <groupId>com.milaboratory</groupId>
+            <artifactId>milib</artifactId>
+            <version>${milib.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>com.milaboratory</groupId>
+            <artifactId>milib</artifactId>
+            <version>${milib.version}</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.beust</groupId>
+            <artifactId>jcommander</artifactId>
+            <version>1.48</version>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.10</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-all</artifactId>
+            <version>1.9.5</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
     <developers>
         <developer>
             <id>dbolotin</id>
@@ -90,43 +127,6 @@
         </developer>
     </developers>
 
-    <dependencies>
-        <dependency>
-            <groupId>com.milaboratory</groupId>
-            <artifactId>milib</artifactId>
-            <version>1.5-SNAPSHOT</version>
-        </dependency>
-        <dependency>
-            <groupId>com.beust</groupId>
-            <artifactId>jcommander</artifactId>
-            <version>1.48</version>
-            <optional>true</optional>
-        </dependency>
-        <dependency>
-            <groupId>com.milaboratory</groupId>
-            <artifactId>milib</artifactId>
-            <version>1.0.1</version>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <version>4.10</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.mockito</groupId>
-            <artifactId>mockito-all</artifactId>
-            <version>1.9.5</version>
-            <scope>test</scope>
-        </dependency>
-    </dependencies>
-
-    <properties>
-        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    </properties>
-
     <scm>
         <connection>scm:git:https://github.com/milaboratory/mitools.git</connection>
     </scm>
@@ -185,6 +185,47 @@
 
     <build>
         <plugins>
+            <plugin>
+                <!-- Workaround maven not being able to set a property conditionally -->
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-antrun-plugin</artifactId>
+                <version>1.8</version>
+                <executions>
+                    <execution>
+                        <id>read_hostname</id>
+                        <phase>validate</phase>
+                        <goals>
+                            <goal>run</goal>
+                        </goals>
+                        <configuration>
+                            <exportAntProperties>true</exportAntProperties>
+                            <target>
+                                <exec executable="hostname" failonerror="false" outputproperty="hostname"/>
+                                <condition property="hostname" value="unknown">
+                                    <not>
+                                        <isset property="hostname"/>
+                                    </not>
+                                </condition>
+                            </target>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>delete_tokens</id>
+                        <phase>process-sources</phase>
+                        <goals>
+                            <goal>run</goal>
+                        </goals>
+                        <configuration>
+                            <tasks>
+                                <delete>
+                                    <fileset dir="${basedir}/src/main/java/" includes="*.tokens"/>
+                                </delete>
+                            </tasks>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>buildnumber-maven-plugin</artifactId>
@@ -206,6 +247,7 @@
                         <configuration>
                             <properties>
                                 <branch>${scmBranch}</branch>
+                                <host>${hostname}</host>
                             </properties>
                         </configuration>
                     </execution>
@@ -239,27 +281,6 @@
                 </configuration>
             </plugin>
 
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-antrun-plugin</artifactId>
-                <version>1.7</version>
-                <executions>
-                    <execution>
-                        <phase>process-sources</phase>
-                        <goals>
-                            <goal>run</goal>
-                        </goals>
-                        <configuration>
-                            <tasks>
-                                <delete>
-                                    <fileset dir="${basedir}/src/main/java/" includes="*.tokens"/>
-                                </delete>
-                            </tasks>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
-
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-shade-plugin</artifactId>

diff --git a/src/main/java/com/milaboratory/mitools/cli/Main.java b/src/main/java/com/milaboratory/mitools/cli/Main.java
@@ -32,6 +32,7 @@ public void handle(Signal signal) {
         JCommanderBasedMain main = new JCommanderBasedMain("mitools",
                 new MergeAction(),
                 new TrimAction(),
+                new RandomizeAction(),
                 new RCAction(),
                 new RenameAction(),
                 new SplitAction(),
@@ -54,6 +55,8 @@ public void run() {
                         .append(mitools.getRevision())
                         .append("; branch=")
                         .append(mitools.getBranch())
+                        .append("; host=")
+                        .append(mitools.getHost())
                         .append(")")
                         .append("\n");