added singularity definition file

.gitignore

@@ -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

rules/probabilistic.snk

@@ -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:

singularity_container/ckmertools.def

+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