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
- Name: sonnhammergroup/Domainoid
- License: None
View on Datalad
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 |
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.