-
Notifications
You must be signed in to change notification settings - Fork 4
/
Dockerfile
192 lines (154 loc) · 6.28 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
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
ARG OWNER=jupyter
ARG BASE_CONTAINER=$OWNER/minimal-notebook
FROM $BASE_CONTAINER as base
# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
USER root
RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \
build-essential && \
apt-get clean && rm -rf /var/lib/apt/lists/*
RUN apt update && \
apt-get install -y --no-install-recommends \
man-db \
g++ \
less \
zlib1g-dev \
&& \
apt-get clean && rm -rf /var/lib/apt/lists/*
# out of my way
RUN rm -rf /opt && mkdir /opt
RUN cd /opt && \
git clone --recursive https://github.com/clwgg/seqstats && \
cd seqstats && \
make
# cdbfasta
RUN cd /opt && \
git clone --depth=1 https://github.com/gpertea/cdbfasta.git && \
cd cdbfasta && \
make
# diamond
RUN cd /opt && \
mkdir diamond && \
cd diamond && \
wget http://github.com/bbuchfink/diamond/releases/download/v2.0.15/diamond-linux64.tar.gz && \
tar -xf diamond-linux64.tar.gz && \
rm diamond-linux64.tar.gz
# tsebra
RUN cd /opt && \
git clone https://github.com/Gaius-Augustus/TSEBRA && \
cd TSEBRA && \
git checkout v1.0.3
# makehub
RUN cd /opt && \
git clone https://github.com/Gaius-Augustus/MakeHub.git && \
cd MakeHub && \
git checkout braker3 && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/bedToBigBed && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/genePredCheck && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/faToTwoBit && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/gtfToGenePred && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/hgGcPercent && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/ixIxx && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/twoBitInfo && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/wigToBigWig && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/genePredToBed && \
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/genePredToBigGenePred && \
chmod u+x bedToBigBed genePredCheck faToTwoBit gtfToGenePred hgGcPercent ixIxx twoBitInfo wigToBigWig genePredToBed genePredToBigGenePred make_hub.py
#miniprot
RUN cd /opt && \
git clone --depth=1 https://github.com/lh3/miniprot && \
cd miniprot && \
make
#miniprot-boundary-scorer
RUN cd /opt && \
git clone --depth=1 https://github.com/tomasbruna/miniprot-boundary-scorer.git && \
cd miniprot-boundary-scorer && \
make
#miniprothint
RUN cd /opt && \
git clone --depth=1 https://github.com/tomasbruna/miniprothint.git
# get AUGUSTUS compilation dependencies
# Install required packages
RUN apt-get update
RUN apt-get install -y build-essential wget git autoconf
# Install dependencies for AUGUSTUS comparative gene prediction mode (CGP)
RUN apt-get install -y libgsl-dev libboost-all-dev libsuitesparse-dev liblpsolve55-dev
RUN apt-get install -y libsqlite3-dev libmysql++-dev
# Install dependencies for the optional support of gzip compressed input files
RUN apt-get install -y libboost-iostreams-dev zlib1g-dev
# Install dependencies for bam2hints and filterBam
RUN apt-get install -y libbamtools-dev
# Install additional dependencies for bam2wig
RUN apt-get install -y samtools libhts-dev
# Install additional dependencies for homGeneMapping and utrrnaseq
RUN apt-get install -y libboost-all-dev
# compile augustus from source because of segmentation fault
RUN cd /opt && \
git clone https://github.com/Gaius-Augustus/Augustus.git && \
cd Augustus && \
make && \
cd scripts && \
chmod a+x *.pl && \
chmod a+x *.py
FROM $BASE_CONTAINER
USER root
COPY --from=base /opt/ /opt/
ENV PATH=${PATH}:/opt/seqstats:/opt/cdbfasta:/opt/hisat2:/opt/diamond:/opt/TSEBRA/bin:/opt/MakeHub:/opt/miniprot:/opt/GALBA/scripts:/opt/miniprot-boundary-scorer:/opt/miniprothint
# AUGUSTUS does need several libraries that are now gone, re-install them:
RUN apt-get update --yes && \
apt-get install -y libboost-iostreams-dev zlib1g-dev libboost-all-dev libboost-all-dev libbamtools-dev
ENV AUGUSTUS_CONFIG_PATH=/opt/Augustus/config/
# augustus, install only in order to get the dependencies, will uninstall augustus later on
RUN apt update && \
apt install -yq augustus augustus-data augustus-doc \
# for latex labels
cm-super \
dvipng \
# for matplotlib anim
ffmpeg \
time && \
apt clean all && \
fix-permissions "${AUGUSTUS_CONFIG_PATH}"
# perl & dependencies
RUn apt update && \
apt install -yq libyaml-perl \
libhash-merge-perl \
libparallel-forkmanager-perl \
libscalar-util-numeric-perl \
libclass-data-inheritable-perl \
libexception-class-perl \
libtest-pod-perl \
libfile-which-perl \
libmce-perl \
libthread-queue-perl \
libmath-utils-perl \
libscalar-list-utils-perl && \
apt clean all
USER ${NB_UID}
# only python installations can be done as a normal user
RUN mamba install --quiet -c bioconda -c anaconda --yes \
biopython && \
mamba clean --all -f -y && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
# Pygustus in Pip is at version 0.8.3
RUN pip install pygustus && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
USER root
RUN apt-get remove -y augustus augustus-data augustus-doc
ENV AUGUSTUS_BIN_PATH=/opt/Augustus/bin/
ENV AUGUSTUS_SCRIPTS_PATH=/opt/Augustus/scripts/
ENV PATH=${PATH}:/opt/Augustus/scripts/:/opt/Augustus/bin/
#galba
RUN cd /opt && \
git clone https://github.com/Gaius-Augustus/GALBA.git && \
git clone --depth=1 https://github.com/Gaius-Augustus/BRAKER.git && \
cp BRAKER/scripts/compute_accuracies.sh GALBA/scripts/compute_accuracies.sh && \
cp BRAKER/scripts/compare_intervals_exact.pl GALBA/scripts/compare_intervals_exact.pl
USER ${NB_UID}
WORKDIR "${HOME}"