From 53de0513516991d4de0c5df38ff277be39690f40 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Wed, 6 Aug 2025 14:10:08 +0200
Subject: [PATCH 1/2] feat: added conda env for histograms

---
 workflow/envs/histogram.yml | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 workflow/envs/histogram.yml

diff --git a/workflow/envs/histogram.yml b/workflow/envs/histogram.yml
new file mode 100644
index 0000000..961f3af
--- /dev/null
+++ b/workflow/envs/histogram.yml
@@ -0,0 +1,6 @@
+channels:
+    - conda-forge
+    - bioconda
+dependencies:
+    - python>=3.12.4    
+    - pandas>=2.2.2
\ No newline at end of file

From c3e631701af3ae7001c69c8871c4d4c395868359 Mon Sep 17 00:00:00 2001
From: meesters <meesters@uni-mainz.de>
Date: Wed, 6 Aug 2025 14:26:24 +0200
Subject: [PATCH 2/2] feat: added conda specs to some rules

---
 workflow/envs/biopython.yml                        |  7 +++++++
 workflow/envs/openbabel.yml                        |  4 ++++
 workflow/envs/{histogram.yml => simple_pandas.yml} |  0
 workflow/rules/analyse.smk                         |  6 ++++++
 workflow/rules/preparation.smk                     | 10 ++++++++++
 5 files changed, 27 insertions(+)
 create mode 100644 workflow/envs/biopython.yml
 create mode 100644 workflow/envs/openbabel.yml
 rename workflow/envs/{histogram.yml => simple_pandas.yml} (100%)

diff --git a/workflow/envs/biopython.yml b/workflow/envs/biopython.yml
new file mode 100644
index 0000000..200df86
--- /dev/null
+++ b/workflow/envs/biopython.yml
@@ -0,0 +1,7 @@
+channels:
+    - conda-forge
+    - bioconda
+dependencies:
+    - python>=3.12.4    
+    - biopython >=1.84
+    - pandas>=2.2.2
\ No newline at end of file
diff --git a/workflow/envs/openbabel.yml b/workflow/envs/openbabel.yml
new file mode 100644
index 0000000..c9493cb
--- /dev/null
+++ b/workflow/envs/openbabel.yml
@@ -0,0 +1,4 @@
+channels:
+    - conda-forge
+dependencies:
+    - openbabel>=3.1.1
\ No newline at end of file
diff --git a/workflow/envs/histogram.yml b/workflow/envs/simple_pandas.yml
similarity index 100%
rename from workflow/envs/histogram.yml
rename to workflow/envs/simple_pandas.yml
diff --git a/workflow/rules/analyse.smk b/workflow/rules/analyse.smk
index eb7b05c..5f948c7 100644
--- a/workflow/rules/analyse.smk
+++ b/workflow/rules/analyse.smk
@@ -172,6 +172,8 @@ rule makeHistogram:
         ),
     log:
         "logs/makeHistogram_{receptorID}.log",
+    conda:
+        "../envs/simple_pandas.yml"
     envmodules:
         config["PYPLOT"],
     script:
@@ -214,6 +216,8 @@ rule dockingResultsTxt:
         path.join(OUTPUT_DIR, "results", "{receptorID}_{percentage}.csv"),
     log:
         "logs/dockingResultsTxt_{receptorID}_{percentage}.log",
+    conda:
+        "../envs/simple_pandas.yml"
     wildcard_constraints:
         receptorID="[^/]+",
         percentage="[^/]+",
@@ -420,6 +424,8 @@ rule makeVenn:
             ),
             category="Rescreening",
         ),
+    conda:
+        "../envs/simple_pandas.yml"
     log:
         "logs/makeVenn_{receptorID}_{percentage}.log",
     script:
diff --git a/workflow/rules/preparation.smk b/workflow/rules/preparation.smk
index 303b2b8..7c67023 100644
--- a/workflow/rules/preparation.smk
+++ b/workflow/rules/preparation.smk
@@ -32,6 +32,8 @@ rule convertMol2:
         path.join(INPUT_DIR, "ZINC", "subsets", "{subset}.mol2"),
     output:
         path.join(TMP_DIR, "unzipped", "ZINC", "subsets", "{subset}.pdbqt"),
+    conda:
+        "../envs/openbabel.yml"
     envmodules:
         config["OPENBABEL"],
     shell:
@@ -64,6 +66,8 @@ rule SDFToPDBQT:
         path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "{name}.sdf"),
     output:
         path.join(TMP_DIR, "unzipped", "{database}", "{dataset}", "{name}.pdbqt"),
+    conda:
+        "../envs/openbabel.yml"
     envmodules:
         config["OPENBABEL"],
     shell:
@@ -75,6 +79,8 @@ rule prepareReceptor:
         path.join(TMP_DIR, "unzipped", "PDB", "receptor", "{name}.pdb"),
     output:
         path.join(TMP_DIR, "PDB", "receptor", "{name}.pdb"),
+    conda:
+        "../envs/biopython.yml"
     envmodules:
         config["BIOPYTHON"],
     script:
@@ -86,6 +92,8 @@ rule makeReceptorPDBQT:
         path.join(TMP_DIR, "PDB", "receptor", "{name}.pdb"),
     output:
         path.join(PREPARED_DIR, "receptor", "{name}.pdbqt"),
+    conda:
+        "../envs/openbabel.yml"
     envmodules:
         config["OPENBABEL"],
     shell:
@@ -138,6 +146,8 @@ rule energyMin:
         partition=config["ENERGY_MIN"]["partition"],
         runtime=config["ENERGY_MIN"]["runtime"],
         mem_mb=config["ENERGY_MIN"]["mem_mb"],
+    conda:
+        "../envs/openbabel.yml"
     envmodules:
         config["OPENBABEL"],
     shell: