From da644e0a5aa35a4fc3e757e935d1245d195782ab Mon Sep 17 00:00:00 2001
From: daspacio9 <derekaspacio@gmail.com>
Date: Thu, 3 Apr 2025 07:09:59 -0700
Subject: [PATCH] changed the requirements file to remove pymol, which caused
 dependency errors due to pymol 2.5 being deprecated.

Changed all of the dependencies to be explicit versions that match the liulab workstation maple env
---
 requirements.yaml | 73 +++++++++++++++++++++++------------------------
 1 file changed, 36 insertions(+), 37 deletions(-)

diff --git a/requirements.yaml b/requirements.yaml
index d403aa6..3f4a2b9 100644
--- a/requirements.yaml
+++ b/requirements.yaml
@@ -8,43 +8,42 @@ channels:
   - bokeh
   - schrodinger
 dependencies:
-  - snakemake
-  - python=3.9
-  - minimap2
-  - samtools
-  - ngmerge
+  - snakemake=7.32.3
+  - python=3.9  
+  - minimap2=2.26
+  - samtools=1.17
+  - ngmerge=0.3
   - numba=0.56 # pacmap is broken with numba 0.53, medaka is broken with numba 0.57
-  - setuptools
-  - wget
-  - numpy
-  - pandas
-  - scipy
-  - scikit-learn
-  - statsmodels
-  - biopython
-  - jupyter
-  - jupyter_bokeh
-  - umi_tools
-  - medaka
-  - keras-preprocessing # not installed by medaka in some cases, probably just specific to my machine but doesn't hurt to add
-  - nanoplot
-  - natsort
-  - hvplot
-  - holoviews
-  - datashader
-  - bokeh
-  - spatialpandas # allows for lasso selections of datashaded plots
-  - panel
-  - editdistance
-  - racon
-  - wheel
-  - cython
-  - tqdm
-  - blat # for C3POa
-  - mappy
-  - pymol # not used by pipeline, but nice to have for SequenceAnalyzer
-  - pip
+  - setuptools=68.1.2
+  - wget=1.20.3
+  - numpy=1.23.5
+  - pandas=2.1.0
+  - scipy=1.11.2
+  - scikit-learn=1.3.0
+  - statsmodels=0.14.0
+  - biopython=1.81
+  - jupyter=1.0.0
+  - jupyter_bokeh=3.0.7
+  - umi_tools=1.1.4
+  - keras-preprocessing=1.1.2 # not installed by medaka in some cases, probably just specific to my machine but doesn't hurt to add
+  - nanoplot=1.41.6
+  - natsort=8.4.0
+  - hvplot=0.8.4
+  - holoviews=1.18.1
+  - datashader=0.15.2
+  - bokeh=3.2.2
+  - spatialpandas=0.4.8 # allows for lasso selections of datashaded plots
+  - panel=1.2.1
+  - editdistance=0.6.2
+  - racon=1.5.0
+  - wheel=0.41.2
+  - cython=3.0.2
+  - tqdm=4.66.1
+  - blat=35 # for C3POa
+  - mappy=2.26
+  - pip=23.2.1
+  - medaka=1.8
   - pip:
     - pyabpoa==1.4.0
-    - pacmap
-    - selenium # for bokeh SVG export, conda installation is broken
\ No newline at end of file
+    - pacmap==0.7.0
+    - selenium==4.12.0 # for bokeh SVG export, conda installation is broken
\ No newline at end of file