remove default anaconda channels (#342)

* remove default anaconda channels * use nodefaults in all conda environment files
PGScatalog · Jul 30, 2024 · ad835ae · ad835ae
1 parent 9f675c0
commit ad835ae
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Showing 7 changed files with 18 additions and 7 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -43,7 +43,7 @@ process {
     }
 
     withLabel: plink2 {
-        ext.conda = "bioconda::plink2==2.00a5.10"
+        ext.conda = "$projectDir/environments/plink2/environment.yml"
         ext.docker = 'ghcr.io/pgscatalog/plink2'
         ext.singularity = 'oras://ghcr.io/pgscatalog/plink2'
         ext.docker_version = ':2.00a5.10'
@@ -67,7 +67,7 @@ process {
     }
 
     withLabel: pyyaml {
-        ext.conda = "conda-forge::pyyaml==6.0"
+        ext.conda = "$projectDir/environments/pyyaml/environment.yml"
         ext.singularity = 'oras://ghcr.io/pgscatalog/pyyaml'
         ext.singularity_version = ':6.0-singularity'
         ext.docker = 'ghcr.io/pgscatalog/pyyaml'

diff --git a/environments/fraposa/environment.yml b/environments/fraposa/environment.yml
@@ -2,5 +2,6 @@ name: fraposa-pgsc
 channels:
   - conda-forge
   - bioconda
+  - nodefaults  
 dependencies:
-- fraposa-pgsc=1.0.0
+  - fraposa-pgsc=1.0.0
diff --git a/environments/pgscatalog_utils/environment.yml b/environments/pgscatalog_utils/environment.yml
@@ -2,5 +2,6 @@ name: pgscatalog-utils
 channels:
   - conda-forge
   - bioconda
+  - nodefaults  
 dependencies:
-- pgscatalog-utils=1.2.0
+  - pgscatalog-utils=1.2.0
diff --git a/environments/plink2/environment.yml b/environments/plink2/environment.yml
@@ -0,0 +1,7 @@
+name: plink2
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults  
+dependencies: 
+  - plink2==2.00a5.10
diff --git a/environments/pyyaml/environment.yml b/environments/pyyaml/environment.yml
@@ -2,6 +2,6 @@ name: pyyaml
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
-- pyyaml=6.0.1
+  - pyyaml=6.0.1
diff --git a/environments/report/environment.yml b/environments/report/environment.yml
@@ -2,6 +2,7 @@ name: report
 channels:
   - conda-forge
   - bioconda
+  - nodefaults  
 dependencies: 
   - r-jsonlite
   - r-dplyr

diff --git a/environments/zstd/environment.yml b/environments/zstd/environment.yml
@@ -2,5 +2,6 @@ name: zstd
 channels:
   - conda-forge
   - bioconda
+  - nodefaults  
 dependencies:
-- zstd=1.4.8
+  - zstd=1.4.8