diff --git a/2024.10/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml b/2024.10/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml index ac510f2c..1b725d6e 100644 --- a/2024.10/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml +++ b/2024.10/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml @@ -203,7 +203,7 @@ dependencies: - liblapacke=3.9.0 - libllvm18=18.1.7 - libnghttp2=1.58.0 -- libopenblas=0.3.27 +- libopenblas=0.3.28 - libpng=1.6.43 - libprotobuf=3.20.3 - libsodium=1.0.18 @@ -300,7 +300,7 @@ dependencies: - perl-module-runtime=0.016 - perl-number-format=1.76 - perl-params-validate=1.31 -- perl-parent=0.241 +- perl-parent=0.242 - perl-pathtools=3.75 - perl-readonly=2.05 - perl-regexp-common=2017060201 @@ -354,22 +354,22 @@ dependencies: - pyvcf3=1.0.3 - pyyaml=6.0.2 - pyzmq=24.0.1 -- q2-amrfinderplus=0+untagged.63.g92e9219 -- q2-assembly=2024.10.0.dev0+10.g9b4ab57 -- q2-demux=2024.10.0.dev0+3.g7c9b6d3 -- q2-feature-classifier=2024.10.0.dev0+1.g1caeb30 -- q2-feature-table=2024.10.0.dev0+2.ga4d0e2e -- q2-longitudinal=2024.10.0.dev0+1.g207dda1 -- q2-mystery-stew=2024.10.0.dev0 -- q2-quality-control=2024.10.0.dev0 -- q2-sample-classifier=2024.10.0.dev0 -- q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0+23.g4b9509a -- q2-viromics=0+untagged.23.gc1af303 -- q2-vizard=2024.10.0.dev0+232.gebde89a -- q2cli=2024.10.0.dev0+8.gd86cf68 -- q2templates=2024.10.0.dev0 -- qiime2=2024.10.0.dev0+19.g55aad00 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.0 +- q2templates=2024.10.0 +- qiime2=2024.10.0 - quast=5.2.0 - r-abind=1.4_5 - r-argparser=0.7.2 @@ -486,7 +486,7 @@ dependencies: - r-rmarkdown=2.28 - r-rprojroot=2.0.4 - r-rsqlite=2.3.7 -- r-rstudioapi=0.16.0 +- r-rstudioapi=0.17.1 - r-rvest=1.0.4 - r-sass=0.4.9 - r-scales=1.3.0 @@ -520,7 +520,7 @@ dependencies: - readline=8.2 - referencing=0.35.1 - requests=2.32.3 -- rescript=2024.10.0.dev0+24.g29bf18a +- rescript=2024.10.0 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rpds-py=0.20.0 diff --git a/2024.10/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml b/2024.10/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml index 6caae659..dae7dacf 100644 --- a/2024.10/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml +++ b/2024.10/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml @@ -218,7 +218,7 @@ dependencies: - libnghttp2=1.58.0 - libnsl=2.0.1 - libogg=1.3.5 -- libopenblas=0.3.27 +- libopenblas=0.3.28 - libopus=1.3.1 - libpng=1.6.43 - libpq=16.4 @@ -331,7 +331,7 @@ dependencies: - perl-module-runtime=0.016 - perl-number-format=1.76 - perl-params-validate=1.31 -- perl-parent=0.241 +- perl-parent=0.242 - perl-pathtools=3.75 - perl-readonly=2.05 - perl-regexp-common=2017060201 @@ -387,22 +387,22 @@ dependencies: - pyvcf3=1.0.3 - pyyaml=6.0.2 - pyzmq=24.0.1 -- q2-amrfinderplus=0+untagged.63.g92e9219 -- q2-assembly=2024.10.0.dev0+10.g9b4ab57 -- q2-demux=2024.10.0.dev0+3.g7c9b6d3 -- q2-feature-classifier=2024.10.0.dev0+1.g1caeb30 -- q2-feature-table=2024.10.0.dev0+2.ga4d0e2e -- q2-longitudinal=2024.10.0.dev0+1.g207dda1 -- q2-mystery-stew=2024.10.0.dev0 -- q2-quality-control=2024.10.0.dev0 -- q2-sample-classifier=2024.10.0.dev0 -- q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0+23.g4b9509a -- q2-viromics=0+untagged.23.gc1af303 -- q2-vizard=2024.10.0.dev0+232.gebde89a -- q2cli=2024.10.0.dev0+8.gd86cf68 -- q2templates=2024.10.0.dev0 -- qiime2=2024.10.0.dev0+19.g55aad00 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.0 +- q2templates=2024.10.0 +- qiime2=2024.10.0 - qt-main=5.15.8 - quast=5.2.0 - r-abind=1.4_5 @@ -520,7 +520,7 @@ dependencies: - r-rmarkdown=2.28 - r-rprojroot=2.0.4 - r-rsqlite=2.3.7 -- r-rstudioapi=0.16.0 +- r-rstudioapi=0.17.1 - r-rvest=1.0.4 - r-sass=0.4.9 - r-scales=1.3.0 @@ -555,7 +555,7 @@ dependencies: - referencing=0.35.1 - repeatmasker=4.1.7p1 - requests=2.32.3 -- rescript=2024.10.0.dev0+24.g29bf18a +- rescript=2024.10.0 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rmblast=2.14.1 diff --git a/2024.10/pathogenome/passed/seed-environment-conda.yml b/2024.10/pathogenome/passed/seed-environment-conda.yml index d5616e17..bf43c258 100644 --- a/2024.10/pathogenome/passed/seed-environment-conda.yml +++ b/2024.10/pathogenome/passed/seed-environment-conda.yml @@ -16,25 +16,25 @@ dependencies: - pysam=0.22.1 - python=3.9.19 - python_abi=3.9 -- q2-amrfinderplus=0+untagged.63.g92e9219 -- q2-assembly=2024.10.0.dev0+10.g9b4ab57 -- q2-demux=2024.10.0.dev0+3.g7c9b6d3 -- q2-feature-classifier=2024.10.0.dev0+1.g1caeb30 -- q2-feature-table=2024.10.0.dev0+2.ga4d0e2e -- q2-longitudinal=2024.10.0.dev0+1.g207dda1 -- q2-mystery-stew=2024.10.0.dev0 -- q2-quality-control=2024.10.0.dev0 -- q2-sample-classifier=2024.10.0.dev0 -- q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0+23.g4b9509a -- q2-viromics=0+untagged.23.gc1af303 -- q2-vizard=2024.10.0.dev0+232.gebde89a -- q2cli=2024.10.0.dev0+8.gd86cf68 -- q2templates=2024.10.0.dev0 -- qiime2=2024.10.0.dev0+19.g55aad00 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.0 +- q2templates=2024.10.0 +- qiime2=2024.10.0 - r-base=4.3.3 - r-reticulate=1.36.0 -- rescript=2024.10.0.dev0+24.g29bf18a +- rescript=2024.10.0 - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0 diff --git a/2024.10/pathogenome/released/qiime2-pathogenome-macos-latest-conda.yml b/2024.10/pathogenome/released/qiime2-pathogenome-macos-latest-conda.yml index ac510f2c..11967178 100644 --- a/2024.10/pathogenome/released/qiime2-pathogenome-macos-latest-conda.yml +++ b/2024.10/pathogenome/released/qiime2-pathogenome-macos-latest-conda.yml @@ -1,5 +1,5 @@ channels: -- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed +- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released - conda-forge - bioconda dependencies: @@ -203,7 +203,7 @@ dependencies: - liblapacke=3.9.0 - libllvm18=18.1.7 - libnghttp2=1.58.0 -- libopenblas=0.3.27 +- libopenblas=0.3.28 - libpng=1.6.43 - libprotobuf=3.20.3 - libsodium=1.0.18 @@ -300,7 +300,7 @@ dependencies: - perl-module-runtime=0.016 - perl-number-format=1.76 - perl-params-validate=1.31 -- perl-parent=0.241 +- perl-parent=0.242 - perl-pathtools=3.75 - perl-readonly=2.05 - perl-regexp-common=2017060201 @@ -354,22 +354,22 @@ dependencies: - pyvcf3=1.0.3 - pyyaml=6.0.2 - pyzmq=24.0.1 -- q2-amrfinderplus=0+untagged.63.g92e9219 -- q2-assembly=2024.10.0.dev0+10.g9b4ab57 -- q2-demux=2024.10.0.dev0+3.g7c9b6d3 -- q2-feature-classifier=2024.10.0.dev0+1.g1caeb30 -- q2-feature-table=2024.10.0.dev0+2.ga4d0e2e -- q2-longitudinal=2024.10.0.dev0+1.g207dda1 -- q2-mystery-stew=2024.10.0.dev0 -- q2-quality-control=2024.10.0.dev0 -- q2-sample-classifier=2024.10.0.dev0 -- q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0+23.g4b9509a -- q2-viromics=0+untagged.23.gc1af303 -- q2-vizard=2024.10.0.dev0+232.gebde89a -- q2cli=2024.10.0.dev0+8.gd86cf68 -- q2templates=2024.10.0.dev0 -- qiime2=2024.10.0.dev0+19.g55aad00 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.0 +- q2templates=2024.10.0 +- qiime2=2024.10.0 - quast=5.2.0 - r-abind=1.4_5 - r-argparser=0.7.2 @@ -486,7 +486,7 @@ dependencies: - r-rmarkdown=2.28 - r-rprojroot=2.0.4 - r-rsqlite=2.3.7 -- r-rstudioapi=0.16.0 +- r-rstudioapi=0.17.1 - r-rvest=1.0.4 - r-sass=0.4.9 - r-scales=1.3.0 @@ -520,7 +520,7 @@ dependencies: - readline=8.2 - referencing=0.35.1 - requests=2.32.3 -- rescript=2024.10.0.dev0+24.g29bf18a +- rescript=2024.10.0 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rpds-py=0.20.0 diff --git a/2024.10/pathogenome/released/qiime2-pathogenome-ubuntu-latest-conda.yml b/2024.10/pathogenome/released/qiime2-pathogenome-ubuntu-latest-conda.yml index 6caae659..22401d11 100644 --- a/2024.10/pathogenome/released/qiime2-pathogenome-ubuntu-latest-conda.yml +++ b/2024.10/pathogenome/released/qiime2-pathogenome-ubuntu-latest-conda.yml @@ -1,5 +1,5 @@ channels: -- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed +- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released - conda-forge - bioconda dependencies: @@ -218,7 +218,7 @@ dependencies: - libnghttp2=1.58.0 - libnsl=2.0.1 - libogg=1.3.5 -- libopenblas=0.3.27 +- libopenblas=0.3.28 - libopus=1.3.1 - libpng=1.6.43 - libpq=16.4 @@ -331,7 +331,7 @@ dependencies: - perl-module-runtime=0.016 - perl-number-format=1.76 - perl-params-validate=1.31 -- perl-parent=0.241 +- perl-parent=0.242 - perl-pathtools=3.75 - perl-readonly=2.05 - perl-regexp-common=2017060201 @@ -387,22 +387,22 @@ dependencies: - pyvcf3=1.0.3 - pyyaml=6.0.2 - pyzmq=24.0.1 -- q2-amrfinderplus=0+untagged.63.g92e9219 -- q2-assembly=2024.10.0.dev0+10.g9b4ab57 -- q2-demux=2024.10.0.dev0+3.g7c9b6d3 -- q2-feature-classifier=2024.10.0.dev0+1.g1caeb30 -- q2-feature-table=2024.10.0.dev0+2.ga4d0e2e -- q2-longitudinal=2024.10.0.dev0+1.g207dda1 -- q2-mystery-stew=2024.10.0.dev0 -- q2-quality-control=2024.10.0.dev0 -- q2-sample-classifier=2024.10.0.dev0 -- q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0+23.g4b9509a -- q2-viromics=0+untagged.23.gc1af303 -- q2-vizard=2024.10.0.dev0+232.gebde89a -- q2cli=2024.10.0.dev0+8.gd86cf68 -- q2templates=2024.10.0.dev0 -- qiime2=2024.10.0.dev0+19.g55aad00 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.0 +- q2templates=2024.10.0 +- qiime2=2024.10.0 - qt-main=5.15.8 - quast=5.2.0 - r-abind=1.4_5 @@ -520,7 +520,7 @@ dependencies: - r-rmarkdown=2.28 - r-rprojroot=2.0.4 - r-rsqlite=2.3.7 -- r-rstudioapi=0.16.0 +- r-rstudioapi=0.17.1 - r-rvest=1.0.4 - r-sass=0.4.9 - r-scales=1.3.0 @@ -555,7 +555,7 @@ dependencies: - referencing=0.35.1 - repeatmasker=4.1.7p1 - requests=2.32.3 -- rescript=2024.10.0.dev0+24.g29bf18a +- rescript=2024.10.0 - rfc3339-validator=0.1.4 - rfc3986-validator=0.1.1 - rmblast=2.14.1 diff --git a/2024.10/pathogenome/released/seed-environment-conda.yml b/2024.10/pathogenome/released/seed-environment-conda.yml index d5616e17..3412762e 100644 --- a/2024.10/pathogenome/released/seed-environment-conda.yml +++ b/2024.10/pathogenome/released/seed-environment-conda.yml @@ -1,5 +1,5 @@ channels: -- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed +- https://packages.qiime2.org/qiime2/2024.10/pathogenome/released - conda-forge - bioconda dependencies: @@ -16,25 +16,25 @@ dependencies: - pysam=0.22.1 - python=3.9.19 - python_abi=3.9 -- q2-amrfinderplus=0+untagged.63.g92e9219 -- q2-assembly=2024.10.0.dev0+10.g9b4ab57 -- q2-demux=2024.10.0.dev0+3.g7c9b6d3 -- q2-feature-classifier=2024.10.0.dev0+1.g1caeb30 -- q2-feature-table=2024.10.0.dev0+2.ga4d0e2e -- q2-longitudinal=2024.10.0.dev0+1.g207dda1 -- q2-mystery-stew=2024.10.0.dev0 -- q2-quality-control=2024.10.0.dev0 -- q2-sample-classifier=2024.10.0.dev0 -- q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0+23.g4b9509a -- q2-viromics=0+untagged.23.gc1af303 -- q2-vizard=2024.10.0.dev0+232.gebde89a -- q2cli=2024.10.0.dev0+8.gd86cf68 -- q2templates=2024.10.0.dev0 -- qiime2=2024.10.0.dev0+19.g55aad00 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.0 +- q2templates=2024.10.0 +- qiime2=2024.10.0 - r-base=4.3.3 - r-reticulate=1.36.0 -- rescript=2024.10.0.dev0+24.g29bf18a +- rescript=2024.10.0 - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0 diff --git a/2024.10/pathogenome/staged/seed-environment-conda.yml b/2024.10/pathogenome/staged/seed-environment-conda.yml index f46e6b0d..8532ae13 100644 --- a/2024.10/pathogenome/staged/seed-environment-conda.yml +++ b/2024.10/pathogenome/staged/seed-environment-conda.yml @@ -16,25 +16,25 @@ dependencies: - pysam=0.22.1 - python=3.9.19 - python_abi=3.9 -- q2-amrfinderplus=0+untagged.63.g92e9219 -- q2-assembly=2024.10.0.dev0+10.g9b4ab57 -- q2-demux=2024.10.0.dev0+3.g7c9b6d3 -- q2-feature-classifier=2024.10.0.dev0+1.g1caeb30 -- q2-feature-table=2024.10.0.dev0+2.ga4d0e2e -- q2-longitudinal=2024.10.0.dev0+1.g207dda1 -- q2-mystery-stew=2024.10.0.dev0 -- q2-quality-control=2024.10.0.dev0 -- q2-sample-classifier=2024.10.0.dev0 -- q2-taxa=2024.10.0.dev0 -- q2-types=2024.10.0.dev0+23.g4b9509a -- q2-viromics=0+untagged.23.gc1af303 -- q2-vizard=2024.10.0.dev0+232.gebde89a -- q2cli=2024.10.0.dev0+8.gd86cf68 -- q2templates=2024.10.0.dev0 -- qiime2=2024.10.0.dev0+19.g55aad00 +- q2-amrfinderplus=2024.10.0 +- q2-assembly=2024.10.0 +- q2-demux=2024.10.0 +- q2-feature-classifier=2024.10.0 +- q2-feature-table=2024.10.0 +- q2-longitudinal=2024.10.0 +- q2-mystery-stew=2024.10.0 +- q2-quality-control=2024.10.0 +- q2-sample-classifier=2024.10.0 +- q2-taxa=2024.10.0 +- q2-types=2024.10.0 +- q2-viromics=2024.10.0 +- q2-vizard=2024.10.0 +- q2cli=2024.10.0 +- q2templates=2024.10.0 +- qiime2=2024.10.0 - r-base=4.3.3 - r-reticulate=1.36.0 -- rescript=2024.10.0.dev0+24.g29bf18a +- rescript=2024.10.0 - scikit-bio=0.6.0 - scikit-learn=1.4.2 - scipy=1.13.0