updated conda path

metagenlab · Aug 2, 2024 · 9e1031e · 9e1031e
1 parent 8b461f0
commit 9e1031e
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Showing 4 changed files with 15 additions and 15 deletions.
diff --git a/zamp/rules/DB_processing/DB_preprocessing.rules b/zamp/rules/DB_processing/DB_preprocessing.rules
@@ -4,7 +4,7 @@
 
 rule Extract_amplicons_cutadapt:
     conda:
-        "../../envs/cutadapt.yml"
+        os.path.join(dir.envs, "cutadapt.yml")
     container:
         singularity_envs["cutadapt"]
     input:
@@ -37,7 +37,7 @@ rule Extract_amplicons_cutadapt:
 
 rule Dereplicate_amplicons:
     conda:
-        "../../envs/vsearch.yml"
+        os.path.join(dir.envs, "vsearch.yml")
     container:
         singularity_envs["vsearch"]
     input:
@@ -60,7 +60,7 @@ rule Dereplicate_amplicons:
 
 rule Derep_and_merge_taxonomy:
     conda:
-        "../../envs/pandas.yml"
+        os.path.join(dir.envs, "pandas.yml")
     container:
         singularity_envs["pandas"]
     input:

diff --git a/zamp/rules/DB_processing/DB_skip_preprocessing.rules b/zamp/rules/DB_processing/DB_skip_preprocessing.rules
@@ -16,7 +16,7 @@ rule copy_fasta:
 
 rule clean_unprocessed_DB_taxonomy:
     conda:
-        "../../envs/pandas.yml"
+        os.path.join(dir.envs, "pandas.yml")
     container:
         singularity_envs["pandas"]
     input:

diff --git a/zamp/rules/DB_processing/RDP_validation.rules b/zamp/rules/DB_processing/RDP_validation.rules
@@ -5,7 +5,7 @@
 ### C) plot inta taxon similarity
 rule Visualize_similarity_rdp:  ## Generate a plot for intra taxa similarity. Very long to compute 
     conda:
-        "../../envs/rdp_classifier.yml"
+        os.path.join(dir.envs, "rdp_classifier.yml")
     container:
         singularity_envs["rdp_classifier"]
     input:
@@ -35,7 +35,7 @@ rule Visualize_similarity_rdp:  ## Generate a plot for intra taxa similarity. Ve
 ### D.1) Leave one sequence out test for accuracy testing
 rule Accuracy_seqs_testing_rdp:
     conda:
-        "../../envs/rdp_classifier.yml"
+        os.path.join(dir.envs, "rdp_classifier.yml")
     container:
         singularity_envs["rdp_classifier"]
     input:
@@ -62,7 +62,7 @@ rule Accuracy_seqs_testing_rdp:
 ### D.2) Leave one taxon out test for accuracy testing
 rule Accuracy_taxon_testing_rdp:
     conda:
-        "../../envs/rdp_classifier.yml"
+        os.path.join(dir.envs, "rdp_classifier.yml")
     container:
         singularity_envs["rdp_classifier"]
     input:
@@ -89,7 +89,7 @@ rule Accuracy_taxon_testing_rdp:
 ### E) Cross-validate
 rule Cross_validate__rdp:
     conda:
-        "../../envs/rdp_classifier.yml"
+        os.path.join(dir.envs, "rdp_classifier.yml")
     container:
         singularity_envs["rdp_classifier"]
     input:

diff --git a/zamp/rules/DB_processing/format_n_train_classifiers.rules b/zamp/rules/DB_processing/format_n_train_classifiers.rules
@@ -1,7 +1,7 @@
 ## Rules to format the taxonomy into a format for DADA2 implementation of RDP.
 rule DADA2_prep_tax_db:
     conda:
-        "../../envs/amplicons_r_utils.yml"
+        os.path.join(dir.envs, "amplicons_r_utils.yml")
     container:
         singularity_envs["r_utils"]
     input:
@@ -40,7 +40,7 @@ rule Hash_DADA2:
 
 rule Preformat_for_cannonical_rdp:
     conda:
-        "../../envs/amplicons_r_utils.yml"
+        os.path.join(dir.envs, "amplicons_r_utils.yml")
     container:
         singularity_envs["r_utils"]
     input:
@@ -57,7 +57,7 @@ rule Preformat_for_cannonical_rdp:
 
 rule Format_rdp_lineages:
     conda:
-        "../../envs/python.yml"
+        os.path.join(dir.envs, "python.yml")
     container:
         singularity_envs["python"]
     input:
@@ -74,7 +74,7 @@ rule Format_rdp_lineages:
 
 rule Format_rdp_add_lineages:
     conda:
-        "../../envs/python.yml"
+        os.path.join(dir.envs, "python.yml")
     container:
         singularity_envs["python"]
     input:
@@ -99,7 +99,7 @@ def get_mem_mb(mem):
 
 rule Train_rdp_classifier:
     conda:
-        "../../envs/rdp_classifier.yml"
+        os.path.join(dir.envs, "rdp_classifier.yml")
     container:
         singularity_envs["rdp_classifier"]
     input:
@@ -145,7 +145,7 @@ rule Hash_RDP:
 ## Rules to format the taxonomy into a format for DADA2 implementation of RDP.
 rule Decipher_prep_fasta:
     conda:
-        "../../envs/amplicons_r_utils.yml"
+        os.path.join(dir.envs, "amplicons_r_utils.yml")
     container:
         singularity_envs["r_utils"]
     input:
@@ -162,7 +162,7 @@ rule Decipher_prep_fasta:
 
 rule Decipher_train_tax:
     conda:
-        "../../envs/decipher.yml"
+        os.path.join(dir.envs, "decipher.yml")
     container:
         singularity_envs["decipher"]
     input: