ikmb-denbi/genome-annotation:latest
$ singularity pull shub://ikmb-denbi/genome-annotation:latest
Singularity Recipe
Bootstrap:docker
From:nfcore/base
%labels
MAINTAINER Marc Hoeppner <m.hoeppner@ikmb.uni-kiel.de>
DESCRIPTION Singularity image containing all requirements for the annotation pipeline
VERSION 0.1
%environment
PATH=/opt/conda/envs/genome-annotation-1.0/bin:/opt/conda/envs/genome-annotation-1.0/opt/pasa-2.3.3/bin:/opt/bin:$PATH
export PATH
PERL5LIB=$PERL5LIB:/usr/local/share/perl/5.24.1
export PERL5LIB
PASAHOME=/opt/conda/envs/genome-annotation-1.0/opt/pasa-2.3.3
export PASAHOME
EVM_HOME=/opt/conda/envs/genome-annotation-1.0/opt/evidencemodeler-1.1.1
export EVM_HOME
%files
environment.yml /
%post
/opt/conda/bin/conda env create -f /environment.yml
/opt/conda/bin/conda clean -a
# Prereqs for Nextflow
apt-get -y install procps make gcc
cpan -i inc::latest URI::Encode
# Create mount point for RZCluster
mkdir -p /ifs
# Create the default config file
cp /opt/conda/envs/genome-annotation-1.0/opt/pasa-2.3.3/pasa_conf/pasa.CONFIG.template /opt/conda/envs/genome-annotation-1.0/opt/pasa-2.3.3/pasa_conf/conf.txt
# Install rapid fasta splitter
mkdir -p /opt/bin && cd /opt/bin && wget -q ftp://saf.bio.caltech.edu/pub/software/molbio/fastasplitn.c && gcc -o fastasplitn fastasplitn.c && chmod +x fastasplitn
# Install local Blast+ to circumvent buggy version shipping with RepeatMasker
mkdir /opt/blast+ && cd /opt/blast+ && wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-x64-linux.tar.gz && tar -xvf ncbi-blast-2.10.0+-x64-linux.tar.gz && \
rm *.tar.gz && mv ncbi-blast-2.10.0+ 2.10.0
Collection
- Name: ikmb-denbi/genome-annotation
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/ikmb-denbi-genome-annotation-latest |
collection name | ikmb-denbi/genome-annotation |
branch | tblastn-revert |
tag | latest |
commit | 3e0a83e9b9bb4bdd3f00980845919fcac9adc80e |
version (container hash) | c05b6f1e7449010a9afca4ce9cbafa5b |
build date | 2020-04-03T12:27:38.462Z |
size (MB) | 6325.0 |
size (bytes) | 1746927647 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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