afonsoguerra/SnpEffWrapper:latest
$ singularity pull shub://afonsoguerra/SnpEffWrapper:latest
Singularity Recipe
Bootstrap: docker
From: python:3
%labels
Topic VariantEffect
%post
#This is based on debian buster...
apt-get update --fix-missing && apt-get install -y python-pip git openjdk-11-jdk
cd /
git clone --depth=50 --branch=master https://github.com/afonsoguerra/SnpEffWrapper.git sanger-pathogens/SnpEffWrapper
cd sanger-pathogens/SnpEffWrapper
bash install_dependencies.sh
rm -rf /sanger-pathogens/SnpEffWrapper/build/clinEff/
rm -rf /sanger-pathogens/SnpEffWrapper/build/*.zip
pip install /sanger-pathogens/SnpEffWrapper
%runscript
#export SNPEFF_EXEC=/sanger-pathogens/SnpEffWrapper/build/snpEff_v4_1l_core/snpEff.jar
#exec snpEffBuildAndRun --snpeff-exec /sanger-pathogens/SnpEffWrapper/build/snpEff_v4_1l_core/snpEff.jar --java-exec /usr/bin/java "$@"
export SNPEFF_EXEC=/sanger-pathogens/SnpEffWrapper/build/snpEff_v4_3t_core/snpEff.jar
exec snpEffBuildAndRun --snpeff-exec /sanger-pathogens/SnpEffWrapper/build/snpEff_v4_3t_core/snpEff.jar --java-exec /usr/bin/java "$@"
Collection
- Name: afonsoguerra/SnpEffWrapper
- License: GNU General Public License v3.0
View on Datalad
Metrics
key | value |
---|---|
id | /containers/afonsoguerra-SnpEffWrapper-latest |
collection name | afonsoguerra/SnpEffWrapper |
branch | master |
tag | latest |
commit | ca963d6d971b898d884634e531360e23295aced3 |
version (container hash) | d1dd8a6fe47194a7e8629374974eba2b829e1c965b1c7df2b422a6b09287d46e |
build date | 2020-11-18T10:40:11.460Z |
size (MB) | 745.62890625 |
size (bytes) | 781848576 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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