sonnhammergroup/Domainoid:def

$ singularity pull shub://sonnhammergroup/Domainoid:def

Singularity Recipe

Bootstrap: docker
From: ubuntu:latest

%post
apt-get update && apt-get -y install wget build-essential
apt-get install python3 python3-pip bioperl hmmer libmoose-perl git -y
pip3 install biopython networkx sortedcontainers joblib

git clone https://bitbucket.org/sonnhammergroup/domainoid.git /home/domainoid

wget -P  /home/pfam/Pfam  ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.gz
wget -P  /home/pfam/Pfam ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.dat.gz
wget -P  /home/pfam/Pfam ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/active_site.dat.gz
wget -P  /home/pfam ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz

cd /home/pfam
tar xvfz PfamScan.tar.gz

cd /home/pfam/Pfam
gunzip -d Pfam-A.hmm.gz
gunzip -d Pfam-A.hmm.dat.gz
gunzip -d active_site.dat.gz
hmmpress Pfam-A.hmm

wget -P  /home/blast ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.18/blast-2.2.18-x64-linux.tar.gz
cd /home/blast
tar xvfz blast-2.2.18-x64-linux.tar.gz 

cp -a /home/blast/blast-2.2.18/bin/. /home/domainoid/inParanoid
cp /home/blast/blast-2.2.18/data/BLOSUM45 /home/domainoid/inParanoid
cp /home/blast/blast-2.2.18/data/BLOSUM62 /home/domainoid/inParanoid
cp /home/blast/blast-2.2.18/data/BLOSUM80 /home/domainoid/inParanoid
cp /home/blast/blast-2.2.18/data/PAM30 /home/domainoid/inParanoid
cp /home/blast/blast-2.2.18/data/PAM70 /home/domainoid/inParanoid

%environment
export PATH=.:$PATH
export LC_ALL=C
export LANGUAGE=C

%runscript
cd /home/domainoid/
echo "Running: $*"
python3 runDomainoid.py "$@"

Collection


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Metrics

key value
id /containers/sonnhammergroup-Domainoid-def
collection name sonnhammergroup/Domainoid
branch master
tag def
commit b3567341f5a553ec647df39614f363dc1b7dfcff
version (container hash) 82f412030c3a2e1e7ade5b290d22867a
build date 2021-02-05T15:08:52.597Z
size (MB) 4646
size (bytes) 1612140575
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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