More pinned models

kipoi · Apr 1, 2021 · 142c5e5 · 142c5e5
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commit 142c5e5
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Showing 10 changed files with 30 additions and 40 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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: