# HG changeset patch
# User da-intersect
# Date 1367884925 14400
# Node ID 14ccf446423ad2f91f015e556807f8ee9615db56
# Parent  2c43e7613b2f34ef2f2f062e88814982019c428e
Remove the "jars" folder

diff -r 2c43e7613b2f -r 14ccf446423a jars/protein_generator.jar
Binary file jars/protein_generator.jar has changed
diff -r 2c43e7613b2f -r 14ccf446423a jars/results_analyser.jar
Binary file jars/results_analyser.jar has changed
diff -r 2c43e7613b2f -r 14ccf446423a jars/samifier.jar
Binary file jars/samifier.jar has changed
diff -r 2c43e7613b2f -r 14ccf446423a jars/virtual_protein_merger.jar
Binary file jars/virtual_protein_merger.jar has changed
diff -r 2c43e7613b2f -r 14ccf446423a protein_generator.sh
--- a/protein_generator.sh	Tue Apr 30 21:59:55 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-#!/bin/bash
-
-if (type -p java >> /dev/null); then
-    _java=java
-elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]];  then
-    _java="$JAVA_HOME/bin/java"
-else
-    echo "You must install java before runing this tool" >&2
-    exit 1
-fi
-
-if [[ "$_java" ]]; then
-    version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}')
-    if ! [[ "$version" > "1.6" ]]; then
-        echo "Java version should be > 1.6" >&2
-	exit 1
-    fi
-fi
-
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-
-jar_path="${DIR}/jars/${1}"
-shift
-
-java -Xmx3072M -jar $jar_path $@
diff -r 2c43e7613b2f -r 14ccf446423a protein_merger.sh
--- a/protein_merger.sh	Tue Apr 30 21:59:55 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-# Check java version
-if (type -p java >> /dev/null); then
-    _java=java
-elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]];  then
-    _java="$JAVA_HOME/bin/java"
-else
-    echo "You must install java before runing this tool"
-    exit 1
-fi
-if [[ "$_java" ]]; then
-    version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}')
-    if ! [[ "$version" > "1.6" ]]; then
-        echo "Java version should be > 1.6"
-	exit 1
-    fi
-fi
-
-# Locate the jar directory
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-jar_path="${DIR}/jars/${1}"
-shift
-
-# Untar the chromosome file into a temporary directory
-tar_file="$1"
-shift
-tmp_dir="/tmp/$(basename "$tar_file")"
-mkdir -p $tmp_dir
-tar -C $tmp_dir -xvf $tar_file
-
-# Run the jar and remove the temporary directory
-java -Xmx3072M -jar $jar_path $@ -c "$tmp_dir"
-rm -rf $tmp_dir
diff -r 2c43e7613b2f -r 14ccf446423a result_analyser.sh
--- a/result_analyser.sh	Tue Apr 30 21:59:55 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-# Check java version
-if (type -p java >> /dev/null); then
-    _java=java
-elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]];  then
-    _java="$JAVA_HOME/bin/java"
-else
-    echo "You must install java before runing this tool"
-    exit 1
-fi
-if [[ "$_java" ]]; then
-    version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}')
-    if ! [[ "$version" > "1.6" ]]; then
-        echo "Java version should be > 1.6"
-	exit 1
-    fi
-fi
-
-# Locate the jar directory
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-jar_path="${DIR}/jars/${1}"
-shift
-
-# Untar the chromosome file into a temporary directory
-tar_file="$1"
-shift
-tmp_dir="/tmp/$(basename "$tar_file")"
-mkdir -p $tmp_dir
-tar -C $tmp_dir -xvf $tar_file
-
-# Run the jar and remove the temporary directory
-java -Xmx3072M -jar $jar_path $@ -c "$tmp_dir"
-rm -rf $tmp_dir
diff -r 2c43e7613b2f -r 14ccf446423a samifier.sh
--- a/samifier.sh	Tue Apr 30 21:59:55 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-# Check java version
-if (type -p java >> /dev/null); then
-    _java=java
-elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]];  then
-    _java="$JAVA_HOME/bin/java"
-else
-    echo "You must install java before runing this tool"
-    exit 1
-fi
-if [[ "$_java" ]]; then
-    version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}')
-    if ! [[ "$version" > "1.6" ]]; then
-        echo "Java version should be > 1.6"
-	exit 1
-    fi
-fi
-
-# Locate the jar directory
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-jar_path="${DIR}/jars/${1}"
-shift
-
-# Untar the chromosome file into a temporary directory
-tar_file="$1"
-shift
-tmp_dir="/tmp/$(basename "$tar_file")"
-mkdir -p $tmp_dir
-tar -C $tmp_dir -xvf $tar_file
-
-# Run the jar and remove the temporary directory
-java -Xmx3072M -jar $jar_path $@ -c "$tmp_dir"
-rm -rf $tmp_dir