From 6984677a5dbdfb8f622f2e39dd93617af1fc1480 Mon Sep 17 00:00:00 2001
From: Jonas Birkelund Nilsson <jonasbirkelund@hotmail.com>
Date: Tue, 11 Mar 2025 11:59:56 +0100
Subject: [PATCH] Fix the environment

---
 Snakefile                            |  6 ++++++
 envs/basic_dependencies.yaml         | 20 ++++++++++++--------
 scripts/I_filter_impact.staircase.py |  2 +-
 3 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/Snakefile b/Snakefile
index 6eb29e8..11e4b1c 100644
--- a/Snakefile
+++ b/Snakefile
@@ -55,6 +55,8 @@ rule grid_search:
         valid_df = rules.eval_clonotypes.output.data
     output:
         grid = RES_DIR + "/eval_clonotypes/grid_search/{ext_thr}.csv"
+    conda:
+        "envs/basic_dependencies.yaml"
     shell:
         "python scripts/G1_grid_search.py \
             --input {input.valid_df} \
@@ -72,6 +74,8 @@ rule extract_optimal_threshold:
     output:
         plots = expand(PLT_DIR + "/eval_clonotypes/grid_search/grid.{ext}", ext=["pdf", "png"]),
         opt_thr = RES_DIR + "/eval_clonotypes/threshold/opt.csv"
+    conda:
+        "envs/basic_dependencies.yaml"
     shell:
         "python scripts/G2_extract_optimal_threshold.py \
             --data {input.valid} \
@@ -92,6 +96,8 @@ rule get_filters:
     output:
         lbl = RES_DIR + "/eval_clonotypes/threshold/{filtering_set}.yaml",
         flt = RES_DIR + "/eval_clonotypes/threshold/{filtering_set}.csv"
+    conda:
+        "envs/basic_dependencies.yaml"
     shell:
         "python scripts/H_set_filters.py \
             --data {input.valid} \
diff --git a/envs/basic_dependencies.yaml b/envs/basic_dependencies.yaml
index 0cbd658..95565cf 100755
--- a/envs/basic_dependencies.yaml
+++ b/envs/basic_dependencies.yaml
@@ -1,12 +1,16 @@
+name: basic_dependencies
 channels:
   - conda-forge
-  - conda
   - bioconda
+  - defaults
 dependencies:
-  - pandas = 1.3.3
-  - numpy = 1.19.2
-  - matplotlib = 3.0.3 #3.3.4 #
-  - seaborn = 0.11.2 #0.10.1 #
-  - openpyxl = 3.0.7
-  - numexpr = 2.7.3
-  - pyyaml = 5.1
+  - python=3.10
+  - numpy=1.23.0
+  - pandas=1.3.5
+  - matplotlib=3.5.1
+  - pyyaml=6.0
+  - snakemake=7.32.4
+  - scipy=1.11.4
+  - pip
+  - pip:
+      - seaborn
diff --git a/scripts/I_filter_impact.staircase.py b/scripts/I_filter_impact.staircase.py
index c7e0250..bcd96c2 100644
--- a/scripts/I_filter_impact.staircase.py
+++ b/scripts/I_filter_impact.staircase.py
@@ -143,7 +143,7 @@ def modify_legend(h,l):
     ax.set_xticklabels([])
     if save:
         plt.savefig(title, bbox_inches='tight', dpi=100)
-    plt.show()
+    #plt.show()
 
 
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