From 536f6bf06c02546ad2d0c07d7d47c9b74c3dc23e Mon Sep 17 00:00:00 2001
From: DerThorsten <derthorstenbeier@gmail.com>
Date: Mon, 29 Jul 2019 12:55:33 +0200
Subject: [PATCH 1/4] added pip to acceptor

---
 MMSplice/modules/acceptor/model.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/MMSplice/modules/acceptor/model.yaml b/MMSplice/modules/acceptor/model.yaml
index c4f382ccf..fcb4ea0de 100644
--- a/MMSplice/modules/acceptor/model.yaml
+++ b/MMSplice/modules/acceptor/model.yaml
@@ -18,6 +18,8 @@ info:
     tags:
         - RNA splicing
 dependencies:
+    conda:
+      - pip
     pip:
         - tensorflow>=1.0.0
         - keras>=2.0.4

From f59c16a934287d107167ec0ab0a61782d6acef5c Mon Sep 17 00:00:00 2001
From: DerThorsten <derthorstenbeier@gmail.com>
Date: Mon, 29 Jul 2019 12:56:18 +0200
Subject: [PATCH 2/4] pinned acceptor

---
 MMSplice/modules/acceptor/dataloader.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MMSplice/modules/acceptor/dataloader.yaml b/MMSplice/modules/acceptor/dataloader.yaml
index 36451fda5..c30fc3d29 100644
--- a/MMSplice/modules/acceptor/dataloader.yaml
+++ b/MMSplice/modules/acceptor/dataloader.yaml
@@ -70,7 +70,7 @@ dependencies:
     - python=3.5
   pip:
     - kipoi
-    - mmsplice
+    - mmsplice==0.27
 output_schema:
     inputs:
       ss:

From 9a0cc94532231742b3a1156d49b125f2dd8d3f16 Mon Sep 17 00:00:00 2001
From: DerThorsten <derthorstenbeier@gmail.com>
Date: Mon, 29 Jul 2019 12:57:00 +0200
Subject: [PATCH 3/4] pinned labranchor py

---
 labranchor/dataloader.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/labranchor/dataloader.yaml b/labranchor/dataloader.yaml
index 9e8744c7d..f3684f8b3 100644
--- a/labranchor/dataloader.yaml
+++ b/labranchor/dataloader.yaml
@@ -15,7 +15,7 @@ args:
 defined_as: dataloader.py::BranchPointDataset
 dependencies:
   conda:
-  - python
+  - python==3.6
   pip:
   - pysam
   - numpy

From 36aef28dba27bc92b05cb45794f77e03ea204b0b Mon Sep 17 00:00:00 2001
From: DerThorsten <derthorstenbeier@gmail.com>
Date: Mon, 29 Jul 2019 13:31:41 +0200
Subject: [PATCH 4/4] changed dependecies

---
 MMSplice/modules/acceptor/dataloader.yaml      | 2 +-
 MMSplice/modules/donor/dataloader.yaml         | 2 +-
 MMSplice/modules/exon_3prime/dataloader.yaml   | 2 +-
 MMSplice/modules/exon_5prime/dataloader.yaml   | 2 +-
 MMSplice/modules/intron_3prime/dataloader.yaml | 2 +-
 MMSplice/modules/intron_5prime/dataloader.yaml | 2 +-
 labranchor/model.yaml                          | 1 +
 7 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/MMSplice/modules/acceptor/dataloader.yaml b/MMSplice/modules/acceptor/dataloader.yaml
index c30fc3d29..a5bc80404 100644
--- a/MMSplice/modules/acceptor/dataloader.yaml
+++ b/MMSplice/modules/acceptor/dataloader.yaml
@@ -70,7 +70,7 @@ dependencies:
     - python=3.5
   pip:
     - kipoi
-    - mmsplice==0.27
+    - mmsplice==0.2.7
 output_schema:
     inputs:
       ss:
diff --git a/MMSplice/modules/donor/dataloader.yaml b/MMSplice/modules/donor/dataloader.yaml
index ad9e0dd16..b2cb02b7a 100644
--- a/MMSplice/modules/donor/dataloader.yaml
+++ b/MMSplice/modules/donor/dataloader.yaml
@@ -70,7 +70,7 @@ dependencies:
     - python=3.5
   pip:
     - kipoi
-    - mmsplice
+    - mmsplice==0.2.7
 output_schema:
     inputs:
       ss:
diff --git a/MMSplice/modules/exon_3prime/dataloader.yaml b/MMSplice/modules/exon_3prime/dataloader.yaml
index 202b1fbb7..a7bf6eec5 100644
--- a/MMSplice/modules/exon_3prime/dataloader.yaml
+++ b/MMSplice/modules/exon_3prime/dataloader.yaml
@@ -70,7 +70,7 @@ dependencies:
     - python=3.5
   pip:
     - kipoi
-    - mmsplice
+    - mmsplice==0.2.7
 output_schema:
     inputs:
       input_4:
diff --git a/MMSplice/modules/exon_5prime/dataloader.yaml b/MMSplice/modules/exon_5prime/dataloader.yaml
index f3634c629..f6bb9be77 100644
--- a/MMSplice/modules/exon_5prime/dataloader.yaml
+++ b/MMSplice/modules/exon_5prime/dataloader.yaml
@@ -70,7 +70,7 @@ dependencies:
     - python=3.5
   pip:
     - kipoi
-    - mmsplice
+    - mmsplice==0.2.7
 output_schema:
     inputs:
       input_3:
diff --git a/MMSplice/modules/intron_3prime/dataloader.yaml b/MMSplice/modules/intron_3prime/dataloader.yaml
index 201fb2d64..e9f20f469 100644
--- a/MMSplice/modules/intron_3prime/dataloader.yaml
+++ b/MMSplice/modules/intron_3prime/dataloader.yaml
@@ -70,7 +70,7 @@ dependencies:
     - python=3.5
   pip:
     - kipoi
-    - mmsplice
+    - mmsplice==0.2.7
 output_schema:
     inputs:
       input_5:
diff --git a/MMSplice/modules/intron_5prime/dataloader.yaml b/MMSplice/modules/intron_5prime/dataloader.yaml
index 59602734a..881919679 100644
--- a/MMSplice/modules/intron_5prime/dataloader.yaml
+++ b/MMSplice/modules/intron_5prime/dataloader.yaml
@@ -70,7 +70,7 @@ dependencies:
     - python=3.5
   pip:
     - kipoi
-    - mmsplice
+    - mmsplice==0.2.7
 output_schema:
     inputs:
       input_15:
diff --git a/labranchor/model.yaml b/labranchor/model.yaml
index 12ff4ca35..9ccbc4cd5 100644
--- a/labranchor/model.yaml
+++ b/labranchor/model.yaml
@@ -9,6 +9,7 @@ default_dataloader: .
 dependencies:
   conda:
   - pip
+  - bioconda::pysam
   pip:
   - tensorflow>=1.0.0
   - keras>=2.0.4