eilon-s/sherlock_pVACseq:latest
$ singularity pull shub://eilon-s/sherlock_pVACseq:latest
Singularity Recipe
Bootstrap: docker
From: eilons/pvacseq-docker
%help
This is a singularity file for running pVACtools with local installation of IEDB predictors.
%environment
LANGUAGE=en_US
LANG="en_US.UTF-8"
LC_ALL=C
PERL_MM_USE_DEFAULT=1
export LANGUAGE LANG LC_ALL PERL_MM_USE_DEFAUL
%post
# install mhc_i predictors
wget http://downloads.iedb.org/tools/mhci/LATEST-PACKAGE;
mv LATEST-PACKAGE latest_mhc_i.tar.gz;
tar -xzf latest_mhc_i.tar.gz;
# setting to python2
cd mhc_i;
find . -type f -exec perl -pi -e 's/\/bin\/env python/\/bin\/python2.7/' {} \;
find . -type f -exec perl -pi -e 's/\/bin\/python$/\/bin\/python2.7/' {} \;
./configure;
cd ..;
#installing mhc_ii
wget http://downloads.iedb.org/tools/mhcii/LATEST-PACKAGE;
mv LATEST-PACKAGE latest_mhc_ii.tar.gz;
tar -xzf latest_mhc_ii.tar.gz;
# setting to python2
cd mhc_ii;
find . -type f -exec perl -pi -e 's/\/bin\/env python/\/bin\/python2.7/' {} \; ;
find . -type f -exec perl -pi -e 's/\/bin\/python$/\/bin\/python2.7/' {} \; ;
sed -i -- 's/python /python2 /g' mhc_II_binding.py;
sed -i -- 's/python /python2 /g' configure.py;
cd ..;
# downloading test data
#pip install --upgrade pip;
#pip install pvactools;
#pvacseq download_example_data .;
%runscript
exec pvacseq "$@"
# old code to document the versions that were used
#wget http://downloads.iedb.org/tools/mhci/LATEST/IEDB_MHC_I-2.17.tar.gz;
#wget http://downloads.iedb.org/tools/mhci/LATEST/IEDB_MHC_I-2.19.tar.gz;
#tar -xzf IEDB_MHC_I-2.19.tar.gz;
#wget http://downloads.iedb.org/tools/mhcii/LATEST/IEDB_MHC_II-2.17.3.tar.gz;
#wget http://downloads.iedb.org/tools/mhcii/LATEST/IEDB_MHC_II-2.17.5.tar.gz;
#tar -xzf IEDB_MHC_II-2.17.5.tar.gz;
# fixing IEDB???
#sed -i -- 's/.replace("\/"\,"-")//g' mhc_II_binding.py
Collection
- Name: eilon-s/sherlock_pVACseq
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/eilon-s-sherlock_pVACseq-latest |
collection name | eilon-s/sherlock_pVACseq |
branch | master |
tag | latest |
commit | fb18fb0a1886a512f8ab80da2977817552bf7dc2 |
version (container hash) | 6a107cee2d349d9a0cca67f85d27072b |
build date | 2018-05-10T15:50:08.171Z |
size (MB) | None |
size (bytes) | 1624825887 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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