TomHarrop/funannotate-singularity:funannotate_8e2e0a1
$ singularity pull shub://TomHarrop/funannotate-singularity:funannotate_8e2e0a1
Singularity Recipe
Bootstrap: shub
From: TomHarrop/funannotate-singularity:funannotate-deps_8e2e0a1
# Bootstrap: localimage
# From: funannotate-deps_8e2e0a1.sif
%help
'
Funannotate
https://funannotate.readthedocs.io
Funannotate uses environment variables to define the path to the
funannotate database. Override with `-d`, or bind the FUNANNOTATE_DB
directory into the container as follows:
singularity exec \
-B output/funannotate_db:/funannotate_db \
funannotate.sif \
funannotate
The RepeatMasker installation does not include Repbase libraries.
cp the Genemake license to ${HOME}/.gm_key at runtime
The following dependencies have issues in 8e2e0a1
- augustus (installed, not sure what the error is)
- proteinortho not installed, dont know what it is
- salmon (installed at /usr/bin/salmon)
- signalp (not installed, license)
- trimmomatic (installed, java -jar /usr/share/java/trimmomatic.jar,
/usr/bin/TrimmomaticPE, /usr/bin/TrimmomaticSE)
'
%labels
MAINTAINER "Tom Harrop (twharrop@gmail.com)"
VERSION "funannotate 8e2e0a1 for python3"
%post
export DEBIAN_FRONTEND=noninteractive
# Genemark license? cp to ${HOME}/.gm_key at runtime
# funannotate
/usr/local/bin/pip3 \
install \
git+git://github.com/nextgenusfs/funannotate.git@8e2e0a1
export PATH="/blast/bin:${PATH}:/usr/lib/debian-med/bin:/fasta/bin:/pasa/bin:/genemark:/evm:/snap"
export FUNANNOTATE_DB=/funannotate_db
export PASAHOME=/pasa
export TRINITYHOME=/usr/bin
export EVM_HOME=/evm
export AUGUSTUS_CONFIG_PATH="/opt/augustus-3.3.3/config"
export GENEMARK_PATH=/genemark
export BAMTOOLS_PATH=/usr/bin
funannotate check --show-versions
%environment
export PATH="/blast/bin:${PATH}:/usr/lib/debian-med/bin:/fasta/bin:/pasa/bin:/genemark:/evm:/snap"
export FUNANNOTATE_DB=/funannotate_db
export PASAHOME=/pasa
export TRINITYHOME=/usr/bin
export EVM_HOME=/evm
export AUGUSTUS_CONFIG_PATH="/opt/augustus-3.3.3/config"
export GENEMARK_PATH=/genemark
export BAMTOOLS_PATH=/usr/bin
%runscript
exec /usr/local/bin/funannotate "$@"
Collection
- Name: TomHarrop/funannotate-singularity
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/TomHarrop-funannotate-singularity-funannotate_8e2e0a1 |
collection name | TomHarrop/funannotate-singularity |
branch | master |
tag | funannotate_8e2e0a1 |
commit | 38358c6cb6bc998dc4c4c43f548c79d227db0d49 |
version (container hash) | 980fddd07ddecfb9d453c39c4cb3b91c6ed8fc815f471645802f99a1f514f96c |
build date | 2020-02-26T23:35:31.249Z |
size (MB) | 2654.0078125 |
size (bytes) | 2782928896 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
Feedback
Was this page helpful?
Glad to hear it! Please tell us how we can improve.
Sorry to hear that. Please tell us how we can improve.