connor-lab/singularity-recipes:assembly_improvement
$ singularity pull shub://connor-lab/singularity-recipes:assembly_improvement
Singularity Recipe
Bootstrap: docker
From: alpine:3.8
%environment
PATH=$PATH:/usr/local/bin/MUMmer3.23
export PATH
%post
apk update
apk upgrade
apk add bash boost-dev cmake curl db-dev expat-dev g++ gcc gd-dev libxml2-dev make musl-dev perl-app-cpanminus perl-dev zlib-dev
curl -fsSL http://www.cpan.org/authors/id/M/MI/MIROD/XML-DOM-XPath-0.14.tar.gz | tar -xz
cd XML-DOM-XPath-0.14
#sed "s/use encoding 'utf8'/use utf8/g" t/test_non_ascii.t
perl Makefile.PL && make && make install
cd ..
rm -rf XML-DOM-XPath-0.14
cpanm --no-wget -f Bio::AssemblyImprovement
wget https://downloads.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz -O /usr/local/bin/MUMmer3.23.tar.gz
cd /usr/local/bin && tar xvzf MUMmer3.23.tar.gz
cd MUMmer3.23 && make && make install
export PATH=$PATH:/usr/local/bin/MUMmer3.23
cd /tmp/
curl -fsSL https://www.cs.helsinki.fi/u/lmsalmel/Gap2Seq/Gap2Seq-2.1.tar.gz | tar xz
cd Gap2Seq-2.1/
mkdir build; cd build; cmake ..; make
find . -maxdepth 1 -perm /u=x -exec mv {} /usr/local/bin/ \;
chmod 775 /usr/local/bin/Gap2Seq.sh
rm -rf /tmp/Gap2Seq-2.1
Collection
- Name: connor-lab/singularity-recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/connor-lab-singularity-recipes-assembly_improvement |
collection name | connor-lab/singularity-recipes |
branch | master |
tag | assembly_improvement |
commit | 2583535411903625da9ca664dd7548537bbbc2da |
version (container hash) | 3c17b81b554732cfa72077ece599fdbf |
build date | 2019-02-07T15:45:22.882Z |
size (MB) | 877 |
size (bytes) | 193204255 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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