-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile
108 lines (85 loc) · 4.2 KB
/
Dockerfile
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
#FROM alpine
FROM ubuntu:20.04
ENV TZ=Europe/Oslo
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
RUN apt-get update && apt-get install --no-install-recommends --assume-yes -qq curl libncurses5-dev build-essential zlib1g-dev libbz2-dev liblzma-dev unzip default-jre python-is-python3 r-base && apt-get clean
RUN mkdir -p /usr/local/jars/
RUN curl -Lo /tmp/samtools.tgz.bz2 https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2 && \
mkdir /tmp/samtools && \
tar jxvf /tmp/samtools.tgz.bz2 --strip 1 -C /tmp/samtools && \
cd /tmp/samtools && \
./configure --prefix=/usr/local/ && \
make && \
make install && \
rm -rf /tmp/samtools*
RUN curl -Lo /tmp/bcftools.tgz.bz2 https://github.com/samtools/bcftools/releases/download/1.11/bcftools-1.11.tar.bz2 && \
mkdir /tmp/bcftools && \
tar jxvf /tmp/bcftools.tgz.bz2 --strip 1 -C /tmp/bcftools && \
cd /tmp/bcftools && \
./configure --prefix=/usr/local/ && \
make && \
make install && \
rm -rf /tmp/bcftools*
RUN curl -Lo /tmp/htslib.tgz.bz2 https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2 && \
mkdir /tmp/htslib && \
tar jxvf /tmp/htslib.tgz.bz2 --strip 1 -C /tmp/htslib && \
cd /tmp/htslib && \
./configure --prefix=/usr/local/ && \
make && \
make install && \
rm -rf /tmp/htslib*
RUN curl -Lo /tmp/bwa.tgz.bz2 https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2 && \
mkdir /tmp/bwa && \
tar jxvf /tmp/bwa.tgz.bz2 --strip 1 -C /tmp/bwa && \
cd /tmp/bwa && \
make && \
cp bwa /usr/local/bin/bwa && \
rm -rf /tmp/bwa*
RUN curl -Lo /tmp/gatk.zip https://github.com/broadinstitute/gatk/releases/download/4.2.0.0/gatk-4.2.0.0.zip && \
mkdir /usr/local/gatk && \
unzip -d /usr/local/gatk/ /tmp/gatk.zip && \
mv /usr/local/gatk/*/* /usr/local/gatk/ && \
ln -s /usr/local/gatk/gatk /usr/local/bin/gatk && \
rm -f /tmp/gatk.zip
RUN curl -Lo /tmp/star.tgz https://github.com/alexdobin/STAR/archive/2.7.8a.tar.gz && \
mkdir /tmp/star && \
tar zxvf /tmp/star.tgz --strip 1 -C /tmp/star && \
cd /tmp/star/source && \
make && \
cp STAR /usr/local/bin/ && \
rm -rf /tmp/star*
RUN curl -Lo /usr/local/jars/picard.jar https://github.com/broadinstitute/picard/releases/download/2.25.0/picard.jar
RUN curl -Lo /usr/local/bin/verifyBamID https://github.com/statgen/verifyBamID/releases/download/v1.1.3/verifyBamID && \
chmod 755 /usr/local/bin/verifyBamID
RUN curl -Lo /tmp/bedtools.tgz https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools-2.30.0.tar.gz && \
mkdir /tmp/bedtools && \
tar zxvf /tmp/bedtools.tgz --strip 1 -C /tmp/bedtools && \
cd /tmp/bedtools/ && \
make && \
cp bin/* /usr/local/bin/ && \
rm -rf /tmp/bedtools*
RUN curl -Lo /tmp/minimap2.tgz.bz2 https://github.com/lh3/minimap2/releases/download/v2.20/minimap2-2.20.tar.bz2 && \
mkdir /tmp/minimap2 && \
tar jxvf /tmp/minimap2.tgz.bz2 --strip 1 -C /tmp/minimap2 && \
cd /tmp/minimap2 && \
make && \
cp minimap2 /usr/local/bin/minimap2 && \
rm -rf /tmp/minimap2*
RUN curl -Lo /tmp/salmon.tgz https://github.com/COMBINE-lab/salmon/releases/download/v1.5.1/salmon-1.5.1_linux_x86_64.tar.gz && \
mkdir /usr/local/lib/salmon && \
tar zxvf /tmp/salmon.tgz --strip 1 -C /usr/local/lib/salmon && \
ln -s /usr/local/lib/salmon/bin/salmon /usr/local/bin/salmon && \
rm -f /tmp/salmon.tgz
RUN curl -Lo /tmp/fastqc.zip https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip && \
cd /usr/local/lib && \
unzip /tmp/fastqc.zip && \
cd /usr/local/bin && \
ln -s /usr/local/lib/FastQC/fastqc && \
chmod 755 /usr/local/bin/fastqc && \
rm /tmp/fastqc.zip
RUN curl -Lo /tmp/subread.tgz https://sourceforge.net/projects/subread/files/subread-2.0.3/subread-2.0.3-Linux-x86_64.tar.gz/download && \
mkdir -p /tmp/subread && \
tar zxvf /tmp/subread.tgz --strip 1 -C /tmp/subread && \
rm -rf /tmp/subread/bin/utilities && \
cp /tmp/subread/bin/* /usr/local/bin/ && \
rm -rf /tmp/subread*