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feat: adding conda specs #4

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53de051
feat: added conda env for histograms
cmeesters Aug 6, 2025
c3e6317
feat: added conda specs to some rules
cmeesters Aug 6, 2025
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7 changes: 7 additions & 0 deletions workflow/envs/biopython.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
channels:
- conda-forge
- bioconda
dependencies:
- python>=3.12.4
- biopython >=1.84
- pandas>=2.2.2
4 changes: 4 additions & 0 deletions workflow/envs/openbabel.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
channels:
- conda-forge
dependencies:
- openbabel>=3.1.1
6 changes: 6 additions & 0 deletions workflow/envs/simple_pandas.yml
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@@ -0,0 +1,6 @@
channels:
- conda-forge
- bioconda
dependencies:
- python>=3.12.4
- pandas>=2.2.2
6 changes: 6 additions & 0 deletions workflow/rules/analyse.smk
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Expand Up @@ -172,6 +172,8 @@ rule makeHistogram:
),
log:
"logs/makeHistogram_{receptorID}.log",
conda:
"../envs/simple_pandas.yml"
envmodules:
config["PYPLOT"],
script:
Expand Down Expand Up @@ -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="[^/]+",
Expand Down Expand Up @@ -420,6 +424,8 @@ rule makeVenn:
),
category="Rescreening",
),
conda:
"../envs/simple_pandas.yml"
log:
"logs/makeVenn_{receptorID}_{percentage}.log",
script:
Expand Down
10 changes: 10 additions & 0 deletions workflow/rules/preparation.smk
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Expand Up @@ -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:
Expand Down Expand Up @@ -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:
Expand All @@ -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:
Expand All @@ -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:
Expand Down Expand Up @@ -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:
Expand Down