diff --git a/conf/modules.config b/conf/modules.config index 1f345793..b422c3fe 100644 --- 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 index 34612e75..b69cb02a 100644 --- 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 \ No newline at end of file + - fraposa-pgsc=1.0.0 \ No newline at end of file diff --git a/environments/pgscatalog_utils/environment.yml b/environments/pgscatalog_utils/environment.yml index fbf645ed..86c3f114 100644 --- 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 new file mode 100644 index 00000000..1f3bc091 --- /dev/null +++ b/environments/plink2/environment.yml @@ -0,0 +1,7 @@ +name: plink2 +channels: + - conda-forge + - bioconda + - nodefaults +dependencies: + - plink2==2.00a5.10 \ No newline at end of file diff --git a/environments/pyyaml/environment.yml b/environments/pyyaml/environment.yml index 15cb9b73..a7573aff 100644 --- 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 index 9b9bc4b5..43adc80f 100644 --- 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 index 39242d54..856cc981 100644 --- 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