BrendelGroup/AEGeAn:latest
$ singularity pull shub://BrendelGroup/AEGeAn:latest
Singularity Recipe
bootstrap: docker
From: fedora:32
%help
This container provides portable & reproducible components for AEGeAn:
... from the Brendel Group.
Please see https://github.com/BrendelGroup/AEGeAn for complete documentation.
%post
dnf -y update
dnf -y install bc bzip2 findutils git lftp mlocate tcsh unzip zip wget which
dnf -y install gcc-c++ make ruby
dnf -y install cairo-devel pango-devel zlib-devel
dnf -y install libnsl
dnf -y install python3-pycurl python3-pyyaml python3-pandas
dnf -y install python3-entrypoints python3-pytest python3-pytest-cov
dnf -y install python3-biopython
dnf -y install pandoc
dnf -y install parallel
#NOTE: "python" is refered to in AEGeAn code, but may not be defined for
# the Fedora 32 environment as set up above. The following will work:
ln -sf /usr/bin/python3 /usr/bin/python
cd /usr/local/src
echo 'Installing the GenomeTools package:'
git clone https://github.com/genometools/genometools.git
cd genometools
make
make install
make clean
sh -c 'echo "/usr/local/lib" > /etc/ld.so.conf.d/genometools-x86_64.conf'
ldconfig
cd ..
echo 'Installing the cd-hit package:'
git clone https://github.com/weizhongli/cdhit.git
cd cdhit
make
make install
cd ..
echo 'Installing the lastz package:'
mkdir LASTZ
cd LASTZ
wget http://www.bx.psu.edu/~rsharris/lastz/lastz-1.04.03.tar.gz
tar -xzf lastz-1.04.03.tar.gz
cd lastz-distrib-1.04.03/
sed -i -e "1i LASTZ_INSTALL=/usr/local/bin" make-include.mak
sed -i -e "s/-Wall//;" src/Makefile
make
make install
cd ../..
git clone https://github.com/BrendelGroup/AEGeAn.git
cd AEGeAn
make all LocusPocus
make install install-scripts
sh -c 'echo "/usr/local/lib" > /etc/ld.so.conf.d/aegean-x86_64.conf'
ldconfig
cd ..
echo 'Installing BLAST+ version 2.10.1 from NCBI'
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz
tar -xzf ncbi-blast-2.10.1+-x64-linux.tar.gz
cd ncbi-blast-2.10.1+/bin
cp * /usr/local/bin/
cd ../..
rm ncbi-blast-2.10.1+-x64-linux.tar.gz
cd ..
echo 'Installing MuSeqBox version 5.5 from BrendelGroup'
wget http://www.brendelgroup.org/bioinformatics2go/Download/MuSeqBox-3-4-2020.tar.gz
tar -xzf MuSeqBox-3-4-2020.tar.gz
cd MUSEQBOX5.5/src/
make linux
make install
make clean
cd ../..
%environment
export LC_ALL=C
%labels
Maintainer vpbrendel
Version v1.1.0
Collection
- Name: BrendelGroup/AEGeAn
- License: ISC License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/BrendelGroup-AEGeAn-latest |
collection name | BrendelGroup/AEGeAn |
branch | master |
tag | latest |
commit | 4d59d2f268cf67d1296dd3eea52cf76d7a23c465 |
version (container hash) | c4b1dcbddbba1b897b13fb728ec585eb |
build date | 2021-04-18T20:34:13.395Z |
size (MB) | 3213.0 |
size (bytes) | 997421087 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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