This repository has been archived by the owner on Mar 12, 2018. It is now read-only.
forked from nf-core/methylseq
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Dockerfile-bwa
96 lines (82 loc) · 3.49 KB
/
Dockerfile-bwa
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
# openjdk:8 moved from debian jessie to stretch after u131, which breaks everything (bowtie)
FROM openjdk:8u121
LABEL authors="[email protected],[email protected]" \
description="Docker image containing all requirements for NGI-MethylSeq pipeline"
# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
RUN apt-get update && \
apt-get install -y --no-install-recommends \
g++ \
gcc \
gfortran \
libbz2-dev \
libcurl4-openssl-dev \
libgsl0-dev \
liblzma-dev \
libncurses5-dev \
libpcre3-dev \
libreadline-dev \
libssl-dev \
libtbb-dev \
make \
python-dev \
zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*
# Install pip
RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \
python /opt/get-pip.py && \
rm /opt/get-pip.py
RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -o /opt/fastqc_v0.11.5.zip && \
unzip /opt/fastqc_v0.11.5.zip -d /opt/ && \
chmod 755 /opt/FastQC/fastqc && \
ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
rm /opt/fastqc_v0.11.5.zip
# Install cutadapt
RUN pip install cutadapt
# Install TrimGalore
RUN mkdir /opt/TrimGalore && \
curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.zip -o /opt/TrimGalore/0.4.4.zip && \
unzip /opt/TrimGalore/0.4.4.zip -d /opt/TrimGalore && \
ln -s /opt/TrimGalore/TrimGalore-0.4.4/trim_galore /usr/local/bin/trim_galore && \
rm /opt/TrimGalore/0.4.4.zip
# Install SAMTools
RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2 -o /opt/samtools-1.5.tar.bz2 && \
tar xvjf /opt/samtools-1.5.tar.bz2 -C /opt/ && \
cd /opt/samtools-1.5 && \
make && \
make install && \
rm /opt/samtools-1.5.tar.bz2
# Install PicardTools
RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/picard-tools-2.0.1.zip -o /opt/picard-tools-2.0.1.zip && \
unzip /opt/picard-tools-2.0.1.zip -d /opt/ && \
rm /opt/picard-tools-2.0.1.zip
ENV PICARD_HOME /opt/picard-tools-2.0.1
# Install Qualimap
RUN mkdir /opt/Qualimap && \
curl -fsSL https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip -o /opt/Qualimap/qualimap.zip && \
unzip /opt/Qualimap/qualimap.zip -d /opt/Qualimap && \
ln -s /opt/Qualimap/qualimap_v2.2.1/qualimap /usr/local/bin/qualimap && \
rm /opt/Qualimap/qualimap.zip
# Install BWA
RUN mkdir /opt/bwa && \
curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.15.tar.bz2 -o /opt/bwa/bwa.tar.bz2 && \
tar xvjf /opt/bwa/bwa.tar.bz2 -C /opt/bwa/ && \
cd /opt/bwa/bwa-0.7.15/ && \
make && \
ln -s /opt/bwa/bwa-0.7.15/bwa /usr/local/bin/bwa && \
rm /opt/bwa/bwa.tar.bz2
# Install bwa-meth
RUN pip install toolshed && \
pip install git+git://github.com/brentp/bwa-meth.git
# Install MethylDackel
RUN mkdir /opt/MethylDackel && \
curl -fsSL https://github.com/dpryan79/MethylDackel/archive/0.2.1.zip -o /opt/MethylDackel/MethylDackel.zip && \
unzip /opt/MethylDackel/MethylDackel.zip -d /opt/MethylDackel && \
cd /opt/MethylDackel/MethylDackel-0.2.1 && \
make && \
make install prefix=/usr/local/bin && \
rm /opt/MethylDackel/MethylDackel.zip
# Install MultiQC
RUN pip install multiqc
# Create root directories for UPPMAX and c3se hebbe
RUN mkdir /pica /lupus /crex1 /crex2 /proj /scratch /sw \
/c3se /local /apps