diff --git a/BPNet-OSKN/model.yaml b/BPNet-OSKN/model.yaml index db015501a..999904c0a 100644 --- a/BPNet-OSKN/model.yaml +++ b/BPNet-OSKN/model.yaml @@ -34,18 +34,18 @@ dependencies: - bioconda::pysam>=0.14.0 - bioconda::genomelake==0.1.4 - - pytorch::pytorch # optional for data-loading - - cython - - h5py>=2.7.0 - - numpy + - pytorch::pytorch=1.4.0 # optional for data-loading + - cython=0.29.22 + - h5py=2.10.0 + - numpy=1.19.2 - - pandas>=0.23.0 - - fastparquet - - python-snappy - - - nb_conda + - pandas=1.1.5 + - fastparquet=0.5.0 + - python-snappy=0.6.0 + - pip=21.0.1 + - nb_conda=2.2.1 pip: - - tensorflow>=1.0,<1.15 + - tensorflow==1.14.0 - git+https://github.com/kundajelab/DeepExplain.git - keras==2.2.4 - git+https://github.com/kundajelab/bpnet.git@0cb7277b736260f8b4084c9b0c5bd62b9edb5266 diff --git a/CpGenie/merged/model.yaml b/CpGenie/merged/model.yaml index 703a9669f..034a63db6 100644 --- a/CpGenie/merged/model.yaml +++ b/CpGenie/merged/model.yaml @@ -36,11 +36,12 @@ default_dataloader: dummy_axis: 1 dependencies: conda: - - python=3.6 + - python=3.6.12 - h5py=2.10.0 - tensorflow=1.10.0 - keras=1.2.2 - pysam=0.15.3 + - pip=20.2.4 schema: inputs: name: seq diff --git a/CpGenie/model-template.yaml b/CpGenie/model-template.yaml index 16b7949ff..9fb99f8a2 100644 --- a/CpGenie/model-template.yaml +++ b/CpGenie/model-template.yaml @@ -48,10 +48,12 @@ default_dataloader: dummy_axis: 1 dependencies: conda: + - python=3.6.12 - h5py=2.10.0 - tensorflow=1.10.0 - keras=1.2.2 - pysam=0.15.3 + - pip=20.2.4 schema: inputs: name: seq diff --git a/DeepBind/model-template.yaml b/DeepBind/model-template.yaml index 1c6697a16..1d3840fb6 100644 --- a/DeepBind/model-template.yaml +++ b/DeepBind/model-template.yaml @@ -37,11 +37,13 @@ default_dataloader: dependencies: conda: + - python=3.6.12 - h5py=2.10.0 - tensorflow=1.4.1 - keras=2.1.6 - python=3.6 - pysam=0.15.3 + - pip=20.2.4 schema: inputs: name: seq diff --git a/DeepCpG_DNA/Hou2016_HCC_dna/dataloader.yaml b/DeepCpG_DNA/Hou2016_HCC_dna/dataloader.yaml index e3b18d55b..cb7a25bcb 100644 --- a/DeepCpG_DNA/Hou2016_HCC_dna/dataloader.yaml +++ b/DeepCpG_DNA/Hou2016_HCC_dna/dataloader.yaml @@ -12,12 +12,11 @@ args: defined_as: dataloader.py::SeqDataset dependencies: conda: - - bioconda::genomelake==0.1.4 - - bioconda::pybedtools - - python=3.5 - - numpy - - pandas - - cython + - bioconda::genomelake=0.1.4 + - bioconda::pybedtools=0.8.1 + - python=3.6 + - numpy=1.19.2 + - pandas=1.1.3 info: authors: - github: avsecz diff --git a/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml b/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml index d1e074b3f..7a9527e5d 100644 --- a/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml @@ -11,12 +11,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6 + - h5py=2.10.0 + - pip=20.2.4 pip: - - tensorflow==1.4.1 - - keras==1.2.2 - - deepcpg==1.0.4 + - tensorflow==1.10.0 + - keras==1.2.2 info: authors: - github: cangermueller diff --git a/DeepCpG_DNA/Hou2016_HepG2_dna/dataloader.yaml b/DeepCpG_DNA/Hou2016_HepG2_dna/dataloader.yaml index e3b18d55b..15e2427b4 100644 --- a/DeepCpG_DNA/Hou2016_HepG2_dna/dataloader.yaml +++ b/DeepCpG_DNA/Hou2016_HepG2_dna/dataloader.yaml @@ -12,12 +12,11 @@ args: defined_as: dataloader.py::SeqDataset dependencies: conda: - - bioconda::genomelake==0.1.4 - - bioconda::pybedtools - - python=3.5 - - numpy - - pandas - - cython + - bioconda::genomelake=0.1.4 + - bioconda::pybedtools=0.8.1 + - python=3.6 + - numpy=1.19.2 + - pandas=1.1.3 info: authors: - github: avsecz diff --git a/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml b/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml index f73c3cd34..f4f16cd79 100644 --- a/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml @@ -10,12 +10,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6 + - h5py=2.10.0 + - pip=20.2.4 pip: - - tensorflow==1.4.1 - - keras==1.2.2 - - deepcpg==1.0.4 + - tensorflow==1.10.0 + - keras==1.2.2 info: authors: - github: cangermueller diff --git a/DeepCpG_DNA/Hou2016_mESC_dna/dataloader.yaml b/DeepCpG_DNA/Hou2016_mESC_dna/dataloader.yaml index e3b18d55b..15e2427b4 100644 --- a/DeepCpG_DNA/Hou2016_mESC_dna/dataloader.yaml +++ b/DeepCpG_DNA/Hou2016_mESC_dna/dataloader.yaml @@ -12,12 +12,11 @@ args: defined_as: dataloader.py::SeqDataset dependencies: conda: - - bioconda::genomelake==0.1.4 - - bioconda::pybedtools - - python=3.5 - - numpy - - pandas - - cython + - bioconda::genomelake=0.1.4 + - bioconda::pybedtools=0.8.1 + - python=3.6 + - numpy=1.19.2 + - pandas=1.1.3 info: authors: - github: avsecz diff --git a/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml b/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml index b935a2501..bf59e3ac8 100644 --- a/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml @@ -10,12 +10,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6 + - h5py=2.10.0 + - pip=20.2.4 pip: - - tensorflow==1.4.1 - - keras==1.2.2 - - deepcpg==1.0.4 + - tensorflow==1.10.0 + - keras==1.2.2 info: authors: - github: cangermueller diff --git a/DeepCpG_DNA/Smallwood2014_2i_dna/dataloader.yaml b/DeepCpG_DNA/Smallwood2014_2i_dna/dataloader.yaml index e3b18d55b..15e2427b4 100644 --- a/DeepCpG_DNA/Smallwood2014_2i_dna/dataloader.yaml +++ b/DeepCpG_DNA/Smallwood2014_2i_dna/dataloader.yaml @@ -12,12 +12,11 @@ args: defined_as: dataloader.py::SeqDataset dependencies: conda: - - bioconda::genomelake==0.1.4 - - bioconda::pybedtools - - python=3.5 - - numpy - - pandas - - cython + - bioconda::genomelake=0.1.4 + - bioconda::pybedtools=0.8.1 + - python=3.6 + - numpy=1.19.2 + - pandas=1.1.3 info: authors: - github: avsecz diff --git a/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml b/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml index 52bbe6f9a..c871d8990 100644 --- a/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml +++ b/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml @@ -10,12 +10,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6 + - h5py=2.10.0 + - pip=20.2.4 pip: - - tensorflow==1.4.1 - - keras==1.2.2 - - deepcpg==1.0.4 + - tensorflow==1.10.0 + - keras==1.2.2 info: authors: - github: cangermueller diff --git a/DeepCpG_DNA/Smallwood2014_serum_dna/dataloader.yaml b/DeepCpG_DNA/Smallwood2014_serum_dna/dataloader.yaml index e3b18d55b..15e2427b4 100644 --- a/DeepCpG_DNA/Smallwood2014_serum_dna/dataloader.yaml +++ b/DeepCpG_DNA/Smallwood2014_serum_dna/dataloader.yaml @@ -12,12 +12,11 @@ args: defined_as: dataloader.py::SeqDataset dependencies: conda: - - bioconda::genomelake==0.1.4 - - bioconda::pybedtools - - python=3.5 - - numpy - - pandas - - cython + - bioconda::genomelake=0.1.4 + - bioconda::pybedtools=0.8.1 + - python=3.6 + - numpy=1.19.2 + - pandas=1.1.3 info: authors: - github: avsecz diff --git a/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml b/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml index 4683dfdcb..45ddf7ac7 100644 --- a/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml +++ b/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml @@ -10,12 +10,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6 + - h5py=2.10.0 + - pip=20.2.4 pip: - - tensorflow==1.4.1 - - keras==1.2.2 - - deepcpg==1.0.4 + - tensorflow==1.10.0 + - keras==1.2.2 info: authors: - github: cangermueller diff --git a/DeepCpG_DNA/template/dataloader.yaml b/DeepCpG_DNA/template/dataloader.yaml index 5bbcfc351..7436e625e 100644 --- a/DeepCpG_DNA/template/dataloader.yaml +++ b/DeepCpG_DNA/template/dataloader.yaml @@ -16,12 +16,11 @@ info: doc: Dataloader for the DeepCpG. dependencies: conda: - - bioconda::genomelake==0.1.4 - - bioconda::pybedtools - - python=3.5 - - numpy - - pandas - - cython + - bioconda::genomelake=0.1.4 + - bioconda::pybedtools=0.8.1 + - python=3.6 + - numpy=1.19.2 + - pandas=1.1.3 output_schema: inputs: dna: diff --git a/DeepCpG_DNA/template/dataloader_m_template.yaml b/DeepCpG_DNA/template/dataloader_m_template.yaml index 08fcb1e3e..a948808a8 100644 --- a/DeepCpG_DNA/template/dataloader_m_template.yaml +++ b/DeepCpG_DNA/template/dataloader_m_template.yaml @@ -21,14 +21,11 @@ info: doc: Dataloader + target output for the DeepCpG model. dependencies: conda: - - bioconda::genomelake==0.1.4 - - bioconda::pybedtools - - python=3.5 - - numpy - - pandas - pip: - - cython - - deepcpg==1.0.4 + - bioconda::genomelake=0.1.4 + - bioconda::pybedtools=0.8.1 + - python=3.6 + - numpy=1.19.2 + - pandas=1.1.3 output_schema: inputs: dna: diff --git a/DeepCpG_DNA/template/model_template.yaml b/DeepCpG_DNA/template/model_template.yaml index 79806a2d5..5a4bb1bde 100644 --- a/DeepCpG_DNA/template/model_template.yaml +++ b/DeepCpG_DNA/template/model_template.yaml @@ -23,12 +23,12 @@ info: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6 + - h5py=2.10.0 + - pip=20.2.4 pip: - - tensorflow==1.4.1 + - tensorflow==1.10.0 - keras==1.2.2 - - deepcpg==1.0.4 schema: inputs: dna: diff --git a/DeepSEA/beluga/model.yaml b/DeepSEA/beluga/model.yaml index f9824795f..b67a1a9ec 100644 --- a/DeepSEA/beluga/model.yaml +++ b/DeepSEA/beluga/model.yaml @@ -32,8 +32,10 @@ default_dataloader: dependencies: conda: - - h5py - - pytorch::pytorch-cpu>=1.0.0 + - python=3.6.12 + - pip=20.2.4 + - h5py=2.10.0 + - pytorch::pytorch-cpu=1.3.1 pip: - kipoiseq diff --git a/DeepSEA/predict/model.yaml b/DeepSEA/predict/model.yaml index 718b3aa74..3a1c57ce2 100644 --- a/DeepSEA/predict/model.yaml +++ b/DeepSEA/predict/model.yaml @@ -45,8 +45,10 @@ default_dataloader: dtype: np.float32 dependencies: conda: - - h5py - - pytorch::pytorch-cpu>=0.2.0 + - python=3.6.12 + - h5py=2.10.0 + - pytorch::pytorch-cpu=1.3.1 + - pip=20.2.4 pip: - kipoiseq schema: diff --git a/DeepSEA/variantEffects/model.yaml b/DeepSEA/variantEffects/model.yaml index b45d8a615..6c60c73ff 100644 --- a/DeepSEA/variantEffects/model.yaml +++ b/DeepSEA/variantEffects/model.yaml @@ -44,8 +44,10 @@ default_dataloader: dtype: np.float32 dependencies: conda: - - h5py - - pytorch::pytorch-cpu>=0.2.0 + - python=3.6.12 + - h5py=2.10.0 + - pytorch::pytorch-cpu=1.3.1 + - pip=20.2.4 pip: - kipoiseq schema: diff --git a/Framepool/model.yaml b/Framepool/model.yaml index c3da649df..a6c8eed4c 100644 --- a/Framepool/model.yaml +++ b/Framepool/model.yaml @@ -13,6 +13,7 @@ dependencies: - tensorflow=1.13.1 - keras=2.2.4 - h5py=2.9.0 + - pip=20.2.4 pip: - kipoi diff --git a/HAL/model.yaml b/HAL/model.yaml index 00c700962..2a31df065 100644 --- a/HAL/model.yaml +++ b/HAL/model.yaml @@ -8,6 +8,7 @@ dependencies: conda: - numpy=1.19.2 - python=3.6 + - pip=20.2.4 pip: - arrow==0.17.0 - attrs==20.2.0 diff --git a/MMSplice/deltaLogitPSI/model.yaml b/MMSplice/deltaLogitPSI/model.yaml index ff8b39016..cbe69ccb4 100644 --- a/MMSplice/deltaLogitPSI/model.yaml +++ b/MMSplice/deltaLogitPSI/model.yaml @@ -14,6 +14,9 @@ info: tags: - RNA splicing dependencies: + conda: + - python=3.6.13 + - pip=21.0.1 pip: - h5py==2.10.0 - mmsplice==1.0.3 diff --git a/MMSplice/modularPredictions/model.yaml b/MMSplice/modularPredictions/model.yaml index 7c7c06493..b3799fe8e 100644 --- a/MMSplice/modularPredictions/model.yaml +++ b/MMSplice/modularPredictions/model.yaml @@ -14,9 +14,12 @@ info: tags: - RNA splicing dependencies: - pip: - - h5py==2.10.0 - - mmsplice==1.0.3 + conda: + - python=3.6.13 + - pip=21.0.1 + pip: + - h5py==2.10.0 + - mmsplice==1.0.3 schema: inputs: seq: diff --git a/MMSplice/mtsplice/model.yaml b/MMSplice/mtsplice/model.yaml index d3c868113..572886156 100644 --- a/MMSplice/mtsplice/model.yaml +++ b/MMSplice/mtsplice/model.yaml @@ -14,6 +14,9 @@ info: tags: - RNA splicing dependencies: + conda: + - python=3.6.13 + - pip=21.0.1 pip: - h5py==2.10.0 - mmsplice==2.0.0 diff --git a/MMSplice/pathogenicity/model.yaml b/MMSplice/pathogenicity/model.yaml index 07878b803..20df93221 100644 --- a/MMSplice/pathogenicity/model.yaml +++ b/MMSplice/pathogenicity/model.yaml @@ -15,9 +15,12 @@ info: tags: - RNA splicing dependencies: - pip: - - h5py==2.10.0 - - mmsplice==1.0.3 + conda: + - python=3.6.13 + - pip=21.0.1 + pip: + - h5py==2.10.0 + - mmsplice==1.0.3 schema: inputs: seq: diff --git a/MMSplice/splicingEfficiency/model.yaml b/MMSplice/splicingEfficiency/model.yaml index 0116ab418..a1f849e54 100644 --- a/MMSplice/splicingEfficiency/model.yaml +++ b/MMSplice/splicingEfficiency/model.yaml @@ -14,9 +14,12 @@ info: tags: - RNA splicing dependencies: - pip: - - h5py==2.10.0 - - mmsplice==1.0.3 + conda: + - python=3.6.13 + - pip=21.0.1 + pip: + - h5py==2.10.0 + - mmsplice==1.0.3 schema: inputs: seq: diff --git a/MaxEntScan/dataloader.yaml b/MaxEntScan/dataloader.yaml index 51dea2c04..cb6b3ad6f 100644 --- a/MaxEntScan/dataloader.yaml +++ b/MaxEntScan/dataloader.yaml @@ -21,6 +21,7 @@ args: defined_as: dataloader.py::SplicingMaxEntDatasetSpec dependencies: conda: + - pip=20.2.4 - pysam=0.15.2 - python=3.5.6 info: diff --git a/MaxEntScan/model-template.yaml b/MaxEntScan/model-template.yaml index e688825b0..81b9f0ab6 100644 --- a/MaxEntScan/model-template.yaml +++ b/MaxEntScan/model-template.yaml @@ -27,7 +27,8 @@ info: - RNA splicing dependencies: conda: - - bioconda::maxentpy + - pip=20.2.4 + - bioconda::maxentpy=0.0.1 schema: inputs: name: seq diff --git a/Optimus_5Prime/dataloader.yaml b/Optimus_5Prime/dataloader.yaml index 3ec8dd625..b5cf2bc16 100644 --- a/Optimus_5Prime/dataloader.yaml +++ b/Optimus_5Prime/dataloader.yaml @@ -19,11 +19,13 @@ defined_as: dataloader.py::FixedSeq5UtrDl dependencies: conda: - - bioconda::pybedtools + - python=3.6 + - pip=20.2.4 + - bioconda::pybedtools=0.8.1 pip: - kipoi - kipoiseq - - gffutils + - gffutils==0.10.1 info: authors: diff --git a/Optimus_5Prime/model.yaml b/Optimus_5Prime/model.yaml index 7fa073aac..7c3c46ba7 100644 --- a/Optimus_5Prime/model.yaml +++ b/Optimus_5Prime/model.yaml @@ -11,8 +11,10 @@ default_dataloader: . dependencies: conda: - - tensorflow>=1.0.0 - - keras>=2.0.4 + - tensorflow=1.4.1 + - keras=2.1.6 + - python=3.6 + - pip=20.2.4 info: authors: diff --git a/SiSp/model.yaml b/SiSp/model.yaml index e5c32f2f0..6f2562677 100644 --- a/SiSp/model.yaml +++ b/SiSp/model.yaml @@ -12,8 +12,9 @@ default_dataloader: . dependencies: conda: - python=3.6 - - numpy==1.17.4 - - pandas==0.24.2 + - numpy=1.17.4 + - pandas=0.24.2 + - pip=20.2.4 pip: - keras==2.1.6 - tensorflow==1.4.1 diff --git a/deepTarget/model.yaml b/deepTarget/model.yaml index be3debba8..6a65144b0 100644 --- a/deepTarget/model.yaml +++ b/deepTarget/model.yaml @@ -14,10 +14,10 @@ args: defined_as: model.Model dependencies: conda: - - python - - theano - - numpy<=1.12.0 - - pip + - python=3.6.13 + - theano=1.0.4 + - numpy=1.11.3 + - pip=21.0.1 pip: - keras==0.3.3 info: diff --git a/labranchor/model.yaml b/labranchor/model.yaml index 58969e0a0..eedb95f31 100644 --- a/labranchor/model.yaml +++ b/labranchor/model.yaml @@ -8,8 +8,9 @@ args: default_dataloader: . dependencies: conda: - - pip - - bioconda::pysam + - pip=20.2.4 + - python=3.6 + - bioconda::pysam=0.15.3 pip: - tensorflow==1.4.1 - keras==2.1.6