Update conda environments (Release-2024.10/pathogenome)

qiime2 · Oct 24, 2024 · 1e33ee0 · 1e33ee0
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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