-
Notifications
You must be signed in to change notification settings - Fork 0
/
machete
110 lines (104 loc) · 4.54 KB
/
machete
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
FROM centos:centos6
#comes with python/2.7.5
MAINTAINER Gillian Lee Hsieh <[email protected]>
#RUN yum update -y && yum install -y wget git gcc unzip gcc-c++ zlib-devel openssl-devel sqlite-devel bzip2-devel ncurses-devel lapack-dev blas-dev
RUN yum update -y && yum groupinstall -y 'Development Tools' && yum install -y wget \
bzip2-devel \
lapack-dev blas-dev \
ncurses-devel \
openssl-devel \
sqlite-devel \
zlib-devel \
#lapack-dev blas-dev for installing scipy in Python
#Development Tools installs 28 packages, and their dependencies. The number of dependencies installed on a base image of centos:centos6 were 101, notably of which are Perl v5.10.1, git v1.7.1, unzip
ENV DATA=/home/data IndelIndices=IndelIndices HG19exons=HG19exons circularRNApipeline_Standalone=circularRNApipeline_Standalone
RUN mkdir /srv/software
#gcc-c++ needed for running g++ to make tools, such as Bowtie2
#gcc needed for installing Python
RUN git clone https://github.com/nathankw/KNIFE.git /srv/software/knife && \
cd /srv/software/knife && \
git remote add upstream https://github.com/lindaszabo/KNIFE.git && \
git pull
RUN git clone https://github.com/nathankw/MACHETE.git /srv/software/machete && \
cd /srv/software/machete && \
git remote add upstream https://github.com/gillianhsieh/MACHETE && \
git pull
#INSTALL Python 2.7.10
RUN mkdir -p /srv/src/Python /srv/software/Python && \
cd /srv/src/Python && \
wget https://www.python.org/ftp/python/2.7.10/Python-2.7.10.tgz && \
tar -zxf Python-2.7.10.tgz && \
cd Python-2.7.10 && \
./configure --prefix=/srv/software/Python && \
make && \
make install
ENV PATH=/srv/src/software/Python/bin:${PATH}
RUN wget https://bootstrap.pypa.io/get-pip.py && \
python get-pip.py && \
pip install scipy && \
pip install numpy && \
pip install cutadapt
#INSTALL TBB (Threading Building Blocks) from Intel
#Needed for intalling Bowtie1 and Bowtie2 with parallelism enabled (to use the -p argument).
#RUN mkdir /srv/src/TBB && \
# cd /srv/src/TBB && \
# wget https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz && \
# tar -zxf tbb44_20160128oss_src_0.tgz && \
# cd tbb44_20160128oss && \
# gmake && \
# . build/linux_intel64_gcc_cc4.4.7_libc2.12_kernel4.1.19_release/tbbvars.sh
#INSTALL Bowtie1.1.1
RUN mkdir /srv/src/Bowtie1 && \
cd /srv/src/Bowtie1 && \
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/bowtie-1.1.2-src.zip && \
unzip bowtie-1.1.2-src.zip && \
cd bowtie-1.1.2 && \
# make WITH_TBB=1 && \
make && \
make install
#INSTALL Bowtie2 2.2.8
RUN mkdir /srv/src/Bowtie2 && \
cd /srv/src/Bowtie2 && \
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.8/bowtie2-2.2.8-source.zip && \
unzip bowtie2-2.2.8-source.zip && \
cd bowtie2-2.2.8 && \
# make WITH_TBB=1 && \
make && \
make install
#INSTALL R >= 3.0.2
#As stated in https://cran.r-project.org/bin/linux/redhat/README:
# The Fedora RPMs for R have been ported to RHEL by the project Extra Packages for Enterprise Linux (EPEL)
RUN rpm -Uvh http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm && yum install -y R
#Installs R v3.2.3
#INSTALL samtools/1.3. Needed for knife.
RUN mkdir /srv/src/samtools && \
cd /srv/src/samtools && \
wget https://github.com/samtools/samtools/releases/download/1.3/samtools-1.3.tar.bz2 && \
tar -jxf samtools-1.3.tar.bz2 && \
cd samtools-1.3 && \
./configure --without-curses && \
make && \
make install
#perl installation not neccessary since Development Tools, which yum installed earlier, includes Perl v5.10.1.
#INSTALL Perl. Needed for knife. On sherlock v5.10.1, I'll grab the latest, however.
#RUN mkdir /srv/src/Perl && \
# cd /srv/src/Perl && \
# wget http://www.cpan.org/src/5.0/perl-5.22.1.tar.gz && \
# tar -zxf perl-5.22.1.tar.gz && \
# cd perl-5.22.1 && \
# sh Configure -de && \
# make &&
# make install &&
##### ADD KNIFE Data Dependencies
#Note: The directory itself is not copied, just its contents.
#If <dest> does not end with a trailing slash, it will be considered a regular file and the contents of <src> will be written at <dest>.
#If <dest> doesn’t exist, it is created along with all missing directories in its path.
#ADD /${circularRNApipeline_Standalone} ${DATA}/${circularRNApipeline_Standalone}/
#### ADD MACHETE Data Dependencies
#ADD HG19exons. Location of HG19exons was formerly called PICKLEDIR
#ADD /${HG19exons} ${DATA}/${HG19exons}/
#ADD REG_INDEL_INDICES
#RUN mkdir ${DATA}/${IndelIndices}
#ADD /${IndelIndices} ${DATA}/${IndelIndices}/
ENTRYPOINT []
LABEL version="1.0" description="Detects gene fusions"