From 0ea94527e64853ff026f67f57cbdf294bdadc445 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 12:37:39 +0200 Subject: [PATCH 01/12] Update model.yaml --- BPNet-OSKN/model.yaml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) 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 From da8bb785a4eed0c180af4b713256be4d34d5235b Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 13:15:13 +0200 Subject: [PATCH 02/12] Pinnin pip verisons --- CpGenie/model-template.yaml | 2 ++ DeepBind/model-template.yaml | 2 ++ DeepCpG_DNA/template/model_template.yaml | 7 ++++--- DeepSEA/beluga/model.yaml | 6 ++++-- DeepSEA/predict/model.yaml | 6 ++++-- DeepSEA/variantEffects/model.yaml | 6 ++++-- Framepool/model.yaml | 1 + HAL/model.yaml | 1 + labranchor/model.yaml | 5 +++-- 9 files changed, 25 insertions(+), 11 deletions(-) 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/template/model_template.yaml b/DeepCpG_DNA/template/model_template.yaml index 79806a2d5..b6e384312 100644 --- a/DeepCpG_DNA/template/model_template.yaml +++ b/DeepCpG_DNA/template/model_template.yaml @@ -23,10 +23,11 @@ info: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6.12 + - 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: 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/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 From 567ab2cbdcb08770bb8ee9939824cc6a470a49d0 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 13:54:36 +0200 Subject: [PATCH 03/12] More pinned dependencies --- CpGenie/merged/model.yaml | 3 ++- MMSplice/deltaLogitPSI/model.yaml | 3 +++ MMSplice/modularPredictions/model.yaml | 9 ++++++--- MMSplice/mtsplice/model.yaml | 3 +++ MMSplice/pathogenicity/model.yaml | 9 ++++++--- MMSplice/splicingEfficiency/model.yaml | 9 ++++++--- 6 files changed, 26 insertions(+), 10 deletions(-) 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/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: From 49bc598c1e740ecaa0dcfa1eac65bb2969c80a71 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 14:08:24 +0200 Subject: [PATCH 04/12] Pinning more models --- MaxEntScan/model-template.yaml | 2 +- SiSp/model.yaml | 5 +++-- deepTarget/model.yaml | 8 ++++---- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/MaxEntScan/model-template.yaml b/MaxEntScan/model-template.yaml index e688825b0..55143c718 100644 --- a/MaxEntScan/model-template.yaml +++ b/MaxEntScan/model-template.yaml @@ -27,7 +27,7 @@ info: - RNA splicing dependencies: conda: - - bioconda::maxentpy + - bioconda::maxentpy=0.0.1 schema: inputs: name: seq 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: From 6ab7f60e3fd842ed427af6b1e471de0cae11a019 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 14:24:48 +0200 Subject: [PATCH 05/12] More pinned models --- DeepCpG_DNA/Hou2016_HCC_dna/model.yaml | 11 ++++++----- DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml | 11 ++++++----- DeepCpG_DNA/Hou2016_mESC_dna/model.yaml | 11 ++++++----- DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml | 11 ++++++----- DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml | 11 ++++++----- 5 files changed, 30 insertions(+), 25 deletions(-) diff --git a/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml b/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml index d1e074b3f..86873512d 100644 --- a/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml @@ -11,12 +11,13 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6.12 + - 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 + - deepcpg==1.0.4 info: authors: - github: cangermueller diff --git a/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml b/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml index f73c3cd34..82a11e96b 100644 --- a/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml @@ -10,12 +10,13 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6.12 + - 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 + - deepcpg==1.0.4 info: authors: - github: cangermueller diff --git a/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml b/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml index b935a2501..492d72644 100644 --- a/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml @@ -10,12 +10,13 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6.12 + - 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 + - deepcpg==1.0.4 info: authors: - github: cangermueller diff --git a/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml b/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml index 52bbe6f9a..b1c34161b 100644 --- a/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml +++ b/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml @@ -10,12 +10,13 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6.12 + - 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 + - deepcpg==1.0.4 info: authors: - github: cangermueller diff --git a/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml b/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml index 4683dfdcb..47e8b4009 100644 --- a/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml +++ b/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml @@ -10,12 +10,13 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 - - h5py + - python=3.6.12 + - 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 + - deepcpg==1.0.4 info: authors: - github: cangermueller From c0eb028a1927a078d03c7bff07f6505f0c5e59d3 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 15:38:21 +0200 Subject: [PATCH 06/12] More pinned models --- MaxEntScan/dataloader.yaml | 1 + MaxEntScan/model-template.yaml | 1 + 2 files changed, 2 insertions(+) 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 55143c718..81b9f0ab6 100644 --- a/MaxEntScan/model-template.yaml +++ b/MaxEntScan/model-template.yaml @@ -27,6 +27,7 @@ info: - RNA splicing dependencies: conda: + - pip=20.2.4 - bioconda::maxentpy=0.0.1 schema: inputs: From 92428dd4e2a9c35fc1dbf887985a0b2404c7d09d Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 17:05:14 +0200 Subject: [PATCH 07/12] Fixing python mismatches between model and dataloader yaml --- DeepCpG_DNA/Hou2016_HCC_dna/model.yaml | 2 +- DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml | 2 +- DeepCpG_DNA/Hou2016_mESC_dna/model.yaml | 2 +- DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml | 2 +- DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml b/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml index 86873512d..8e85b3096 100644 --- a/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml @@ -11,7 +11,7 @@ args: default_dataloader: . dependencies: conda: - - python=3.6.12 + - python=3.5 - h5py=2.10.0 - pip=20.2.4 pip: diff --git a/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml b/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml index 82a11e96b..965e8f654 100644 --- a/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml @@ -10,7 +10,7 @@ args: default_dataloader: . dependencies: conda: - - python=3.6.12 + - python=3.5 - h5py=2.10.0 - pip=20.2.4 pip: diff --git a/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml b/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml index 492d72644..a103d5c89 100644 --- a/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml @@ -10,7 +10,7 @@ args: default_dataloader: . dependencies: conda: - - python=3.6.12 + - python=3.5 - h5py=2.10.0 - pip=20.2.4 pip: diff --git a/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml b/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml index b1c34161b..d7024abd8 100644 --- a/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml +++ b/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml @@ -10,7 +10,7 @@ args: default_dataloader: . dependencies: conda: - - python=3.6.12 + - python=3.5 - h5py=2.10.0 - pip=20.2.4 pip: diff --git a/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml b/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml index 47e8b4009..9ff5419cc 100644 --- a/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml +++ b/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml @@ -10,7 +10,7 @@ args: default_dataloader: . dependencies: conda: - - python=3.6.12 + - python=3.5 - h5py=2.10.0 - pip=20.2.4 pip: From 6a6d90460f87d13eae2fedabd86f2e9b903c41d5 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 17:08:12 +0200 Subject: [PATCH 08/12] Fixing deepcpg error --- DeepCpG_DNA/template/model_template.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DeepCpG_DNA/template/model_template.yaml b/DeepCpG_DNA/template/model_template.yaml index b6e384312..4909b4025 100644 --- a/DeepCpG_DNA/template/model_template.yaml +++ b/DeepCpG_DNA/template/model_template.yaml @@ -23,7 +23,7 @@ info: default_dataloader: . dependencies: conda: - - python=3.6.12 + - python=3.5 - h5py=2.10.0 - pip=20.2.4 pip: From 8a6144921ea0518e540900d5fc688996dbe0ecd2 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 17:37:50 +0200 Subject: [PATCH 09/12] Fixing Deepcpg --- DeepCpG_DNA/Hou2016_HCC_dna/dataloader.yaml | 11 +++++------ DeepCpG_DNA/Hou2016_HCC_dna/model.yaml | 3 +-- 2 files changed, 6 insertions(+), 8 deletions(-) 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 8e85b3096..7a9527e5d 100644 --- a/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_HCC_dna/model.yaml @@ -11,13 +11,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 + - python=3.6 - h5py=2.10.0 - pip=20.2.4 pip: - tensorflow==1.10.0 - keras==1.2.2 - - deepcpg==1.0.4 info: authors: - github: cangermueller From 142c5e55674ae3780dc12e46977e05d267b58e0c Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 18:02:21 +0200 Subject: [PATCH 10/12] More pinned models --- DeepCpG_DNA/Hou2016_HepG2_dna/dataloader.yaml | 11 +++++------ DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml | 3 +-- DeepCpG_DNA/Hou2016_mESC_dna/dataloader.yaml | 11 +++++------ DeepCpG_DNA/Hou2016_mESC_dna/model.yaml | 3 +-- DeepCpG_DNA/Smallwood2014_2i_dna/dataloader.yaml | 11 +++++------ DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml | 3 +-- DeepCpG_DNA/Smallwood2014_serum_dna/dataloader.yaml | 11 +++++------ DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml | 3 +-- DeepCpG_DNA/template/dataloader.yaml | 11 +++++------ DeepCpG_DNA/template/model_template.yaml | 3 +-- 10 files changed, 30 insertions(+), 40 deletions(-) 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 965e8f654..f4f16cd79 100644 --- a/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_HepG2_dna/model.yaml @@ -10,13 +10,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 + - python=3.6 - h5py=2.10.0 - pip=20.2.4 pip: - tensorflow==1.10.0 - keras==1.2.2 - - deepcpg==1.0.4 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 a103d5c89..bf59e3ac8 100644 --- a/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml +++ b/DeepCpG_DNA/Hou2016_mESC_dna/model.yaml @@ -10,13 +10,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 + - python=3.6 - h5py=2.10.0 - pip=20.2.4 pip: - tensorflow==1.10.0 - keras==1.2.2 - - deepcpg==1.0.4 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 d7024abd8..c871d8990 100644 --- a/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml +++ b/DeepCpG_DNA/Smallwood2014_2i_dna/model.yaml @@ -10,13 +10,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 + - python=3.6 - h5py=2.10.0 - pip=20.2.4 pip: - tensorflow==1.10.0 - keras==1.2.2 - - deepcpg==1.0.4 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 9ff5419cc..45ddf7ac7 100644 --- a/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml +++ b/DeepCpG_DNA/Smallwood2014_serum_dna/model.yaml @@ -10,13 +10,12 @@ args: default_dataloader: . dependencies: conda: - - python=3.5 + - python=3.6 - h5py=2.10.0 - pip=20.2.4 pip: - tensorflow==1.10.0 - keras==1.2.2 - - deepcpg==1.0.4 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/model_template.yaml b/DeepCpG_DNA/template/model_template.yaml index 4909b4025..5a4bb1bde 100644 --- a/DeepCpG_DNA/template/model_template.yaml +++ b/DeepCpG_DNA/template/model_template.yaml @@ -23,13 +23,12 @@ info: default_dataloader: . dependencies: conda: - - python=3.5 + - python=3.6 - h5py=2.10.0 - pip=20.2.4 pip: - tensorflow==1.10.0 - keras==1.2.2 - - deepcpg==1.0.4 schema: inputs: dna: From 85715613da993e4ebb7e641aac666fed54270818 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 18:03:27 +0200 Subject: [PATCH 11/12] Fixed template --- DeepCpG_DNA/template/dataloader_m_template.yaml | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) 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: From 4f3d1f4fc03fc5ea240df0b20c0bc4a3fe5f8984 Mon Sep 17 00:00:00 2001 From: Haimasree Date: Thu, 1 Apr 2021 19:16:11 +0200 Subject: [PATCH 12/12] Pinning Optimus_5prime --- Optimus_5Prime/dataloader.yaml | 6 ++++-- Optimus_5Prime/model.yaml | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) 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: