connor-lab/singularity-recipes:shiver_init
$ singularity pull shub://connor-lab/singularity-recipes:shiver_init
Singularity Recipe
Bootstrap: docker
From: centos:7.5.1804
%post
yum install -y epel-release
yum -y update
yum install -y git make
yum install -y bc bzip2 bzip2-devel gcc ncurses-devel java-1.8.0-openjdk-headless unzip xz-devel zlib-devel
yum install -y python-devel python2-pip
yum install -y python36 python36-devel python36-setuptools
easy_install-3.6 pip
pip2 install biopython
pip3 install pyfastaq
curl -fsSL 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz' | tar -xz -C /usr/local/bin
find /usr/local/bin/ncbi-blast*/bin -maxdepth 1 -executable -type f -exec ln -s {} /usr/local/bin \;
curl -fsSL 'https://mafft.cbrc.jp/alignment/software/mafft-7.407-without-extensions-src.tgz' | tar -xz -C /tmp/
cd /tmp/mafft-7.407-without-extensions/core && make && make install
curl -fsSL 'https://downloads.sourceforge.net/project/smalt/smalt-0.7.6-static.tar.gz' | tar -xz -C /tmp/
cd /tmp/smalt-0.7.6 && ./configure && make && make install
curl -fsSL 'https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2' | tar -xj -C /tmp/
cd /tmp/samtools-1.9 && ./configure && make && make install
curl -fsSL 'http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip' -o /usr/local/bin/Trimmomatic-0.38.zip
cd /usr/local/bin && unzip Trimmomatic-0.38.zip
ln -s /usr/local/bin/Trimmomatic-0.38/trimmomatic-0.38.jar /usr/local/bin
curl -fsSL https://raw.githubusercontent.com/connor-lab/singularity-recipes/master/scripts/trimmomatic -o /usr/local/bin/trimmomatic
chmod 775 /usr/local/bin/trimmomatic
git clone https://github.com/lh3/seqtk.git /tmp/seqtk
cd /tmp/seqtk
make
cd
cp /tmp/seqtk/seqtk /usr/local/bin
rm -rf /tmp/seqtk
git clone https://github.com/ChrisHIV/shiver/ /usr/local/bin/shiver
#cd /usr/local/bin/shiver
#git reset --hard ce3fc9fc05d2f4cef9e5e8ae6ec3f91e490b5165
#curl -fsSL 'https://github.com/ChrisHIV/shiver/archive/v1.3.5.tar.gz' | tar -xz -C /usr/local/bin && mv /usr/local/bin/shiver-1.3.5 /usr/local/bin/shiver
# find /usr/local/bin/shiver -maxdepth 1 -executable -type f -exec cp {} /usr/local/bin \;
# sed -e '/^ThisDir/ s/^#*/#/' -i /usr/local/bin/shiver_*.sh
# sed -i '/^ToolsDir/i ThisDir="/usr/local/bin/shiver"' /usr/local/bin/shiver_*.sh
rm -rf /tmp/seqtk /tmp/samtools* /tmp/smalt* /tmp/mafft*
%environment
LC_ALL=C
export LC_ALL
PATH=$PATH:/usr/local/bin/shiver
export PATH
%runscript
exec shiver_init.sh "$@"
%labels
Maintainer m-bull
Version shiver-latest
Collection
- Name: connor-lab/singularity-recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/connor-lab-singularity-recipes-shiver_init |
collection name | connor-lab/singularity-recipes |
branch | master |
tag | shiver_init |
commit | b688e9001e40f834d33f20fb4734077c5f7a21be |
version (container hash) | 35d4521cd4351cdc5076db0155873080 |
build date | 2019-02-07T19:57:01.397Z |
size (MB) | 1437 |
size (bytes) | 520237087 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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