-
Notifications
You must be signed in to change notification settings - Fork 0
/
bcftools-1.3.1
50 lines (34 loc) · 1.55 KB
/
bcftools-1.3.1
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
#Dockerfile for bcftools 1.3.1 image with polysomy option enabled and also includes htslib 1.3.2
FROM ubuntu:14.04
MAINTAINER Vandhana Krishnan
RUN apt-get update && apt-get install -y \
git \
make \
g++ \
gcc \
###Install dependencies for bcftools 1.3.1 when using htslib 1.3.2: zlib
zlib1g-dev \
###Include below library else Error message : polysomy.c:33:28: fatal error: gsl/gsl_vector.h: No such file or directory #include <gsl/gsl_vector.h>
libgsl0ldbl \
gsl-bin \
libgsl0-dev \
##Resolving Error message: polysomy.o peakfit.o ../htslib/libhts.a -lpthread -lz -lm -ldl -lgsl -lcblas /usr/bin/ld: cannot find -lcblas collect2: error: ld returned 1 exit status so need libcblas.so
libatlas-base-dev
RUN rm /bin/sh && ln -s /bin/bash /bin/sh
RUN cd /opt &&\
mkdir code &&\
cd code &&\
##Get git repository for bcftools-1.3.1 and htslib 1.3.2
git clone git://github.com/samtools/htslib.git --branch 1.3.2 &&\
git clone git://github.com/samtools/bcftools.git --branch 1.3.1 &&\
##Use make in htslib by adding prefix to bcftools path
cd /opt/code/htslib &&\
make prefix=/opt/code/bcftools
RUN cd /opt/code/bcftools &&\
##Optional compilation to enable the polysomy command
make clean && make USE_GPL=1 &&\
make prefix=/opt/code/bcftools install &&\
echo -e "BCFTOOLS_PLUGINS=/opt/code/bcftools/plugins:\$BCFTOOLS_PLUGINS" >> ~/.bashrc
RUN source ~/.bashrc
##ENV BCFTOOLS_PLUGINS /opt/code/bcftools/plugins
ENV PATH /opt/code/bcftools:/opt/code/bcftools/bin:/opt/code/htslib:$PATH