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

added singularity definition file

parent 299690fe
...@@ -7,4 +7,6 @@ config.yaml ...@@ -7,4 +7,6 @@ config.yaml
__pycache__/ __pycache__/
benchmarks/ benchmarks/
logs/ logs/
report/ report/
\ No newline at end of file *.sif
hilbert/
\ No newline at end of file
...@@ -86,7 +86,8 @@ rule calcLikelihoods: ...@@ -86,7 +86,8 @@ rule calcLikelihoods:
gpus = '0', gpus = '0',
walltime = '00:30:00' walltime = '00:30:00'
singularity: singularity:
'docker://phspo/ckmertools:iterationset-tests' 'singularity_container/ckmertools_iterset.sif'
#'docker://phspo/ckmertools:iterationset-tests'
shell: 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}' '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: ...@@ -107,7 +108,8 @@ rule calcLikelihoods_Generative:
k = lambda wildcards: wildcards.kmer, k = lambda wildcards: wildcards.kmer,
e = lambda wildcards,input : extractTsvValue(input.baseError,0,True) e = lambda wildcards,input : extractTsvValue(input.baseError,0,True)
singularity: singularity:
'docker://phspo/ckmertools:latest' 'singularity_container/ckmertools_iterset.sif'
#'docker://phspo/ckmertools:latest'
log: log:
'logs/'+config['input_folder']+'/probabilistic/kmers/{kmer}/{id}/likelihoods.log' 'logs/'+config['input_folder']+'/probabilistic/kmers/{kmer}/{id}/likelihoods.log'
benchmark: 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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