Commit d95f219b authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

added singularity definition file

parent 299690fe
......@@ -7,4 +7,6 @@ config.yaml
__pycache__/
benchmarks/
logs/
report/
\ No newline at end of file
report/
*.sif
hilbert/
\ No newline at end of file
......@@ -86,7 +86,8 @@ rule calcLikelihoods:
gpus = '0',
walltime = '00:30:00'
singularity:
'docker://phspo/ckmertools:iterationset-tests'
'singularity_container/ckmertools_iterset.sif'
#'docker://phspo/ckmertools:iterationset-tests'
shell:
'c_kmertools --e {input.expected} --c {params.cpus} --m 0 --o {input.observed} --kmererror {params.e} --d {params.deviationCutoff} --target {output.likelihoods} --unexpected {output.unexpectedLikelihoods} --log {log} --itersetType {params.itersetType} --hammingdist {input.V_kmers_distances} --kmersindex {input.V_kmers}'
......@@ -107,7 +108,8 @@ rule calcLikelihoods_Generative:
k = lambda wildcards: wildcards.kmer,
e = lambda wildcards,input : extractTsvValue(input.baseError,0,True)
singularity:
'docker://phspo/ckmertools:latest'
'singularity_container/ckmertools_iterset.sif'
#'docker://phspo/ckmertools:latest'
log:
'logs/'+config['input_folder']+'/probabilistic/kmers/{kmer}/{id}/likelihoods.log'
benchmark:
......
Bootstrap: docker
From: phspo/ckmertools:latest
%environment
export PATH=/ckmertools/build:${PATH}
%post
git clone https://github.com/rogersce/cnpy.git
mkdir cnpy/build
cd cnpy/build && git checkout 4e8810b1a8637695171ed346ce68f6984e585ef4
cmake .. && make && make install
cd /ckmertools && git fetch && git checkout iterationset-tests
cd /ckmertools/build && cmake ../ && make
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