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FROM centos:7 AS download-llvm
ENV LLVM_VERSION 9.0.0
RUN mkdir -p /download
WORKDIR /download
RUN curl -OL https://releases.llvm.org/${LLVM_VERSION}/llvm-${LLVM_VERSION}.src.tar.xz &&\
    curl -OL https://releases.llvm.org/${LLVM_VERSION}/cfe-${LLVM_VERSION}.src.tar.xz &&\
    curl -OL https://releases.llvm.org/${LLVM_VERSION}/compiler-rt-${LLVM_VERSION}.src.tar.xz &&\
    curl -OL https://releases.llvm.org/${LLVM_VERSION}/libcxx-${LLVM_VERSION}.src.tar.xz &&\
    curl -OL https://releases.llvm.org/${LLVM_VERSION}/libcxxabi-${LLVM_VERSION}.src.tar.xz &&\
    curl -OL https://releases.llvm.org/${LLVM_VERSION}/libunwind-${LLVM_VERSION}.src.tar.xz &&\

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FROM centos:7
RUN yum update -y
RUN yum install -y tcsh gcc gcc-c++ make autoconf automake libtool openssl-devel memkind-devel libdb-devel ncurses-devel pam-devel libXmu-devel libXpm-devel motif-devel hwloc-devel ant ant-nodeps javacc junit java-1.7.0-openjdk-devel
RUN mkdir -p build
WORKDIR /build
RUN curl -OL https://github.com/son-of-gridengine/sge/archive/819.tar.gz && tar xzf 819.tar.gz
WORKDIR /build/sge-819/source
RUN sh scripts/bootstrap.sh
RUN ./aimk -no-herd -pam
RUN ./aimk -man

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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE KeyboardMappingScheme>
<!-- Written by Qt Creator 4.8.0, 2018-12-15T21:05:52. -->
<mapping>
 <shortcut id="Perforce.DiffCurrent"/>
 <shortcut id="ModelEditor.Action.Explorer.OpenDiagram"/>
 <shortcut id="Macros.ExecuteLastMacro">
  <key value="Alt+R"/>
 </shortcut>
 <shortcut id="Macros.EndMacro">

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VritualBox Guest Addition 5.2.22 Patch for Cent OS 7.6

Original Patch

https://www.virtualbox.org/attachment/ticket/18093/vbox_video_build_rhel76_fix.patch

How to apply

1. Download vboxvide.patch from below
2. Ensure newline is CR LF
3. Change directory to /opt/VBoxGuestAdditions-5.2.22/src/vboxguest-5.2.22/vboxvideo

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FROM centos:7
RUN yum update -y
RUN yum install -y epel-release
RUN yum install -y gcc gcc-c++ make cmake3 cmake fuse-devel openssl-devel zlib-devel bzip2-devel chrpath patchelf
RUN mkdir -p /build
WORKDIR /build
RUN curl -OL https://libzip.org/download/libzip-1.5.1.tar.gz
RUN tar xzf libzip-1.5.1.tar.gz
WORKDIR /build/libzip-1.5.1
ENV PKG_CONFIG_PATH=/usr/local/lib64/pkgconfig:/usr/lib64/pkgconfig LD_LIBRARY_PATH=/usr/local/lib64:/usr/lib64

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#!/usr/bin/env python3
# -*- coding: utf-8 -*-

import argparse
import cyvcf2
import pyfaidx
import sys

def _main():
    parser = argparse.ArgumentParser(description="Simple Repeat Variant Detector")

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#!/usr/bin/env python
# -*- coding: utf-8 -*-
 
import argparse
import ipaddress
import itertools
import subprocess
import tempfile
import os
import signal

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function add_path() {

    if [ ! -d $1 ];then
        return
    fi

    NEWPREFIX=$1

    case ":$PATH:" in
        *":$NEWPREFIX/bin:"*) return;;

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#!/usr/bin/env python3
# -*- coding: utf-8 -*-

import argparse
import csv
import sqlite3
import sys
import datetime
import pytz
import collections

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