aseetharam/braker:latest
$ singularity pull shub://aseetharam/braker:latest
Singularity Recipe
Bootstrap: docker
From: quay.io/biocontainers/braker2:2.1.6--hdfd78af_2
%environment
export PATH=/opt/gmes_linux_64/ProtHint/bin/:${PATH}
export AUGUSTUS_SCRIPTS_PATH=/usr/local/bin
export AUGUSTUS_BIN_PATH=/usr/local/bin
export GENEMARK_PATH=/opt/gmes_linux_64
export ALIGNMENT_TOOL_PATH=/usr/local/bin/
# Register for GeneMark-ES/ET/EP at http://exon.gatech.edu/GeneMark/license_download.cgi (tested with ver 4.65)
# NOTE: the bundled license key expires after 200 days
%post
set -o pipefail -o errexit
readonly GENEMARK_DOWNLOAD_URL=http://topaz.gatech.edu/GeneMark/tmp/GMtool_v3gNp/gmes_linux_64.tar.gz
wget -O - ${GENEMARK_DOWNLOAD_URL} | gzip -dc | tar -C /opt -xf -
mkdir /opt/gm_key
mv /opt/gmes_linux_64/gm_key /opt/gm_key/.gm_key
cd /opt/gmes_linux_64
perl change_path_in_perl_scripts.pl "/usr/bin/env perl"
# https://github.com/gatech-genemark/ProtHint/issues/27
sed -i.bak 's/grep -P/grep/' /opt/gmes_linux_64/ProtHint/bin/prothint.py
sed -i.bak -e 's/readlink -e/realpath/' -e 's/stat --printf/stat -c/' /opt/gmes_linux_64/ProtHint/bin/spalnBatch.sh
%runscript
exec braker.pl "$@"
Collection
- Name: aseetharam/braker
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/aseetharam-braker-latest |
collection name | aseetharam/braker |
branch | master |
tag | latest |
commit | f97c667493e940e71674bec7705f305d063f23a4 |
version (container hash) | 300ebf2e0d568e0ffd74565977d6271b |
build date | 2021-04-16T21:27:56.100Z |
size (MB) | 1075.0 |
size (bytes) | 294858783 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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