From 2349e04a1ae2d292effabce24e5376b38a6398b2 Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Thu, 5 Sep 2024 16:12:24 -0700
Subject: [PATCH 1/8] LANG: add new pathogenome distro

---
 .../passed/seed-environment-conda.yml         | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 2024.10/pathogenome/passed/seed-environment-conda.yml

diff --git a/2024.10/pathogenome/passed/seed-environment-conda.yml b/2024.10/pathogenome/passed/seed-environment-conda.yml
new file mode 100644
index 00000000..665f5233
--- /dev/null
+++ b/2024.10/pathogenome/passed/seed-environment-conda.yml
@@ -0,0 +1,48 @@
+channels:
+- https://packages.qiime2.org/qiime2/2024.10/metagenome/passed
+- conda-forge
+- bioconda
+dependencies:
+- biom-format=2.1.15
+- bowtie2=2.5.1
+- genome-sampler=0.0.0
+- h5py=3.11.0
+- hdf5=1.14.3
+- matplotlib=3.8.4
+- notebook=6.5.5
+- numpy=1.26.4
+- pandas=2.2.2
+- parsl=2024.4.15
+- patsy=0.5.6
+- pysam=0.22.1
+- python=3.9.19
+- python_abi=3.9
+- q2-amr=0.0.0
+- q2-assembly=2024.10.0.dev0
+- q2-demux=2024.10.0.dev0+2.gc13cafb
+- q2-feature-classifier=2024.10.0.dev0+1.g1caeb30
+- q2-feature-table=2024.10.0.dev0+2.ga4d0e2e
+- q2-longitudinal=2024.10.0.dev0
+- q2-mystery-stew=2024.10.0.dev0
+- q2-quality-control=2024.10.0.dev0
+- q2-sample-classifier=2024.10.0.dev0
+- q2-stats=2024.10.0.dev0+1.g6711b86
+- q2-taxa=2024.10.0.dev0
+- q2-types=2024.10.0.dev0+20.g30d8c74
+- q2-viromics=0.0.0
+- q2-vizard=2024.10.0.dev0
+- q2cli=2024.10.0.dev0+5.g76b8d1e
+- q2templates=2024.10.0.dev0
+- qiime2=2024.10.0.dev0+12.g3581493
+- r-base=4.3.3
+- r-reticulate=1.36.0
+- rescript=2024.10.0.dev0+11.g4f7ab4b
+- scikit-bio=0.6.0
+- scikit-learn=1.4.2
+- scipy=1.13.0
+- seaborn=0.12.2
+- unifrac-binaries=1.4
+- unifrac=1.3
+extras:
+  variant_override:
+    qiime2_epoch: '2024.10'

From 1d27d78ef4e9e4e80007abcf1ca30e156cc59df2 Mon Sep 17 00:00:00 2001
From: Liz Gehret <54517601+lizgehret@users.noreply.github.com>
Date: Thu, 5 Sep 2024 16:42:17 -0700
Subject: [PATCH 2/8] DIST: removes genome-sampler

---
 2024.10/pathogenome/passed/seed-environment-conda.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/2024.10/pathogenome/passed/seed-environment-conda.yml b/2024.10/pathogenome/passed/seed-environment-conda.yml
index 665f5233..fe0c27fa 100644
--- a/2024.10/pathogenome/passed/seed-environment-conda.yml
+++ b/2024.10/pathogenome/passed/seed-environment-conda.yml
@@ -5,7 +5,6 @@ channels:
 dependencies:
 - biom-format=2.1.15
 - bowtie2=2.5.1
-- genome-sampler=0.0.0
 - h5py=3.11.0
 - hdf5=1.14.3
 - matplotlib=3.8.4

From e62670843cefa3b3911b7e0371ee5749e1aa6352 Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Fri, 11 Oct 2024 10:47:30 -0700
Subject: [PATCH 3/8] amr -> amrfinderplus & removing stats

---
 2024.10/pathogenome/passed/seed-environment-conda.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/2024.10/pathogenome/passed/seed-environment-conda.yml b/2024.10/pathogenome/passed/seed-environment-conda.yml
index fe0c27fa..8def2a30 100644
--- a/2024.10/pathogenome/passed/seed-environment-conda.yml
+++ b/2024.10/pathogenome/passed/seed-environment-conda.yml
@@ -16,7 +16,7 @@ dependencies:
 - pysam=0.22.1
 - python=3.9.19
 - python_abi=3.9
-- q2-amr=0.0.0
+- q2-amrfinderplus=0.0.0
 - q2-assembly=2024.10.0.dev0
 - q2-demux=2024.10.0.dev0+2.gc13cafb
 - q2-feature-classifier=2024.10.0.dev0+1.g1caeb30
@@ -25,7 +25,6 @@ dependencies:
 - q2-mystery-stew=2024.10.0.dev0
 - q2-quality-control=2024.10.0.dev0
 - q2-sample-classifier=2024.10.0.dev0
-- q2-stats=2024.10.0.dev0+1.g6711b86
 - q2-taxa=2024.10.0.dev0
 - q2-types=2024.10.0.dev0+20.g30d8c74
 - q2-viromics=0.0.0

From a3e8e5b1e1b7e8406f37319af5e21ad84d1736b7 Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Mon, 14 Oct 2024 09:24:27 -0700
Subject: [PATCH 4/8] try with defaults channel

---
 2024.10/pathogenome/passed/seed-environment-conda.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/2024.10/pathogenome/passed/seed-environment-conda.yml b/2024.10/pathogenome/passed/seed-environment-conda.yml
index 8def2a30..b5c271c3 100644
--- a/2024.10/pathogenome/passed/seed-environment-conda.yml
+++ b/2024.10/pathogenome/passed/seed-environment-conda.yml
@@ -2,6 +2,7 @@ channels:
 - https://packages.qiime2.org/qiime2/2024.10/metagenome/passed
 - conda-forge
 - bioconda
+- defaults
 dependencies:
 - biom-format=2.1.15
 - bowtie2=2.5.1

From 1f118fd38ded0e28dae15c3b19589bb751d11f2f Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Mon, 14 Oct 2024 10:49:45 -0700
Subject: [PATCH 5/8] try old channel order (alphabetical)

---
 2024.10/pathogenome/passed/seed-environment-conda.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/2024.10/pathogenome/passed/seed-environment-conda.yml b/2024.10/pathogenome/passed/seed-environment-conda.yml
index b5c271c3..af740169 100644
--- a/2024.10/pathogenome/passed/seed-environment-conda.yml
+++ b/2024.10/pathogenome/passed/seed-environment-conda.yml
@@ -1,7 +1,7 @@
 channels:
 - https://packages.qiime2.org/qiime2/2024.10/metagenome/passed
-- conda-forge
 - bioconda
+- conda-forge
 - defaults
 dependencies:
 - biom-format=2.1.15

From 01ace56f8594026cdf73a6062578bfd4731d4adc Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Tue, 15 Oct 2024 11:29:07 -0600
Subject: [PATCH 6/8] revert channel changes

---
 2024.10/pathogenome/passed/seed-environment-conda.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/2024.10/pathogenome/passed/seed-environment-conda.yml b/2024.10/pathogenome/passed/seed-environment-conda.yml
index af740169..8def2a30 100644
--- a/2024.10/pathogenome/passed/seed-environment-conda.yml
+++ b/2024.10/pathogenome/passed/seed-environment-conda.yml
@@ -1,8 +1,7 @@
 channels:
 - https://packages.qiime2.org/qiime2/2024.10/metagenome/passed
-- bioconda
 - conda-forge
-- defaults
+- bioconda
 dependencies:
 - biom-format=2.1.15
 - bowtie2=2.5.1

From 8bbc1a65f072c8c3c7db8c31bc88e9e65773c5bd Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Wed, 16 Oct 2024 15:49:40 -0600
Subject: [PATCH 7/8] add vsearch pin to address feature-classifier failure

---
 2024.10/pathogenome/passed/seed-environment-conda.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/2024.10/pathogenome/passed/seed-environment-conda.yml b/2024.10/pathogenome/passed/seed-environment-conda.yml
index 8def2a30..1fecc9b9 100644
--- a/2024.10/pathogenome/passed/seed-environment-conda.yml
+++ b/2024.10/pathogenome/passed/seed-environment-conda.yml
@@ -39,6 +39,9 @@ dependencies:
 - scikit-learn=1.4.2
 - scipy=1.13.0
 - seaborn=0.12.2
+# adding this dep to address feature-classifier test failure on osx
+# https://github.com/qiime2/distributions/actions/runs/11351275507/job/31639822132?pr=366#step:9:444
+- vsearch=2.22.1
 - unifrac-binaries=1.4
 - unifrac=1.3
 extras:

From 0faec8601cdb4d835be96c011b60fe351ec7cbda Mon Sep 17 00:00:00 2001
From: q2d2 <q2d2.noreply@gmail.com>
Date: Thu, 17 Oct 2024 22:25:44 +0000
Subject: [PATCH 8/8] Update conda environments
 (Language-add-pathogenome-distro)

---
 .../qiime2-pathogenome-macos-latest-conda.yml | 591 ++++++++++++++++
 ...qiime2-pathogenome-ubuntu-latest-conda.yml | 652 ++++++++++++++++++
 .../passed/seed-environment-conda.yml         |  26 +-
 .../staged/seed-environment-conda.yml         |  47 ++
 4 files changed, 1302 insertions(+), 14 deletions(-)
 create mode 100644 2024.10/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml
 create mode 100644 2024.10/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml
 create mode 100644 2024.10/pathogenome/staged/seed-environment-conda.yml

diff --git a/2024.10/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml b/2024.10/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml
new file mode 100644
index 00000000..29df681a
--- /dev/null
+++ b/2024.10/pathogenome/passed/qiime2-pathogenome-macos-latest-conda.yml
@@ -0,0 +1,591 @@
+channels:
+- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed
+- conda-forge
+- bioconda
+dependencies:
+- _r-mutex=1.0.1
+- anyio=4.6.2.post1
+- appdirs=1.4.4
+- appnope=0.1.4
+- argcomplete=3.5.1
+- argh=0.31.3
+- argon2-cffi=23.1.0
+- argon2-cffi-bindings=21.2.0
+- arrow=1.3.0
+- asttokens=2.4.1
+- atpublic=5.0
+- attrs=24.2.0
+- bcrypt=4.2.0
+- beautifulsoup4=4.12.3
+- bedtools=2.31.1
+- bibtexparser=1.4.2
+- bioconductor-annotationdbi=1.64.1
+- bioconductor-biobase=2.62.0
+- bioconductor-biocfilecache=2.10.1
+- bioconductor-biocgenerics=0.48.1
+- bioconductor-biocio=1.12.0
+- bioconductor-biocparallel=1.36.0
+- bioconductor-biomart=2.58.0
+- bioconductor-biostrings=2.70.1
+- bioconductor-bsgenome=1.70.1
+- bioconductor-data-packages=20231203
+- bioconductor-decontam=1.22.0
+- bioconductor-delayedarray=0.28.0
+- bioconductor-genomeinfodb=1.38.1
+- bioconductor-genomeinfodbdata=1.2.11
+- bioconductor-genomicalignments=1.38.0
+- bioconductor-genomicfeatures=1.54.1
+- bioconductor-genomicranges=1.54.1
+- bioconductor-iranges=2.36.0
+- bioconductor-keggrest=1.42.0
+- bioconductor-matrixgenerics=1.14.0
+- bioconductor-rhtslib=2.4.0
+- bioconductor-rsamtools=2.18.0
+- bioconductor-rtracklayer=1.62.0
+- bioconductor-s4arrays=1.2.0
+- bioconductor-s4vectors=0.40.2
+- bioconductor-sparsearray=1.2.2
+- bioconductor-structuralvariantannotation=1.18.0
+- bioconductor-summarizedexperiment=1.32.0
+- bioconductor-variantannotation=1.48.1
+- bioconductor-xvector=0.42.0
+- bioconductor-zlibbioc=1.48.0
+- biom-format=2.1.15
+- biopython=1.84
+- blast=2.16.0
+- bleach=6.1.0
+- bowtie2=2.5.1
+- brotli=1.1.0
+- brotli-bin=1.1.0
+- brotli-python=1.1.0
+- bwa=0.7.18
+- bwidget=1.9.14
+- bzip2=1.0.8
+- c-ares=1.34.2
+- ca-certificates=2024.8.30
+- cached-property=1.5.2
+- cached_property=1.5.2
+- cairo=1.18.0
+- cctools_osx-64=986
+- certifi=2024.8.30
+- cffi=1.17.1
+- charset-normalizer=3.4.0
+- checkv=1.0.3
+- circos=0.69.9
+- clang=18.1.7
+- clang-18=18.1.7
+- clang_impl_osx-64=18.1.7
+- clang_osx-64=18.1.7
+- clangxx=18.1.7
+- clangxx_impl_osx-64=18.1.7
+- clangxx_osx-64=18.1.7
+- click=8.1.7
+- colorama=0.4.6
+- comm=0.2.2
+- compiler-rt=18.1.7
+- compiler-rt_osx-64=18.1.7
+- conda-pack=0.7.0
+- contourpy=1.3.0
+- cryptography=43.0.1
+- curl=8.8.0
+- cycler=0.12.1
+- debugpy=1.8.7
+- decorator=4.4.2
+- defusedxml=0.7.1
+- diamond=2.1.8
+- dill=0.3.9
+- entrez-direct=22.4
+- entrypoints=0.4
+- exceptiongroup=1.2.2
+- executing=2.1.0
+- expat=2.6.3
+- fastcluster=1.2.6
+- filelock=3.16.1
+- flufl.lock=8.1.0
+- font-ttf-dejavu-sans-mono=2.37
+- font-ttf-inconsolata=3.000
+- font-ttf-source-code-pro=2.038
+- font-ttf-ubuntu=0.83
+- fontconfig=2.14.2
+- fonts-conda-ecosystem=1
+- fonts-conda-forge=1
+- fonttools=4.54.1
+- fqdn=1.5.1
+- freetype=2.12.1
+- fribidi=1.0.10
+- future=1.0.0
+- gettext=0.22.5
+- gettext-tools=0.22.5
+- gffutils=0.10.1
+- gfortran_impl_osx-64=12.3.0
+- gfortran_osx-64=12.3.0
+- giflib=5.2.2
+- glimmerhmm=3.0.4
+- globus-sdk=3.46.0
+- gmp=6.3.0
+- graphite2=1.3.13
+- gridss=2.11.1
+- h5py=3.11.0
+- harfbuzz=8.5.0
+- hdf5=1.14.3
+- hdmedians=0.14.2
+- hmmer=3.4
+- htslib=1.21
+- icu=73.2
+- idna=3.10
+- ijson=3.3.0
+- importlib-metadata=8.5.0
+- importlib-resources=6.4.5
+- importlib_resources=6.4.5
+- iniconfig=2.0.0
+- insilicoseq=2.0.1
+- iow=1.0.5
+- ipykernel=6.29.5
+- ipython=8.18.1
+- ipython_genutils=0.2.0
+- ipywidgets=8.1.5
+- isl=0.26
+- isoduration=20.11.0
+- jedi=0.19.1
+- jinja2=3.1.4
+- joblib=1.4.2
+- jq=1.7.1
+- jsonlines=3.0.0
+- jsonpointer=3.0.0
+- jsonschema=4.23.0
+- jsonschema-specifications=2024.10.1
+- jsonschema-with-format-nongpl=4.23.0
+- jupyter_client=7.4.9
+- jupyter_core=5.7.2
+- jupyter_events=0.10.0
+- jupyter_server=2.14.2
+- jupyter_server_terminals=0.5.3
+- jupyterlab_pygments=0.3.0
+- jupyterlab_widgets=3.0.13
+- k8=0.2.5
+- kcounter=0.1.1
+- kiwisolver=1.4.7
+- kraken2=2.1.3
+- krb5=1.21.3
+- lcms2=2.16
+- ld64_osx-64=711
+- lerc=4.0.0
+- libaec=1.1.3
+- libasprintf=0.22.5
+- libasprintf-devel=0.22.5
+- libblas=3.9.0
+- libbrotlicommon=1.1.0
+- libbrotlidec=1.1.0
+- libbrotlienc=1.1.0
+- libcblas=3.9.0
+- libclang-cpp18.1=18.1.7
+- libcurl=8.8.0
+- libcxx=19.1.2
+- libdeflate=1.20
+- libedit=3.1.20191231
+- libev=4.33
+- libexpat=2.6.3
+- libffi=3.4.2
+- libgd=2.3.3
+- libgettextpo=0.22.5
+- libgettextpo-devel=0.22.5
+- libgfortran=5.0.0
+- libgfortran-devel_osx-64=12.3.0
+- libgfortran5=13.2.0
+- libglib=2.80.2
+- libhwloc=2.11.1
+- libiconv=1.17
+- libidn2=2.3.7
+- libintl=0.22.5
+- libintl-devel=0.22.5
+- libjpeg-turbo=3.0.0
+- liblapack=3.9.0
+- liblapacke=3.9.0
+- libllvm18=18.1.7
+- libnghttp2=1.58.0
+- libopenblas=0.3.27
+- libpng=1.6.43
+- libprotobuf=3.20.3
+- libsodium=1.0.18
+- libsqlite=3.46.0
+- libssh2=1.11.0
+- libtiff=4.6.0
+- libunistring=0.9.10
+- libwebp=1.4.0
+- libwebp-base=1.4.0
+- libxcb=1.15
+- libxml2=2.12.7
+- libxslt=1.1.39
+- libzlib=1.2.13
+- llvm-openmp=19.1.2
+- llvm-tools=18.1.7
+- lxml=5.2.2
+- lz4=4.3.3
+- lz4-c=1.9.4
+- make=4.4.1
+- markupsafe=3.0.1
+- matplotlib=3.8.4
+- matplotlib-base=3.8.4
+- matplotlib-inline=0.1.7
+- megahit=1.2.9
+- minimap2=2.28
+- mistune=3.0.2
+- mpc=1.3.1
+- mpfr=4.2.1
+- mpi=1.0.1
+- munkres=1.1.4
+- natsort=8.4.0
+- nbclassic=1.1.0
+- nbclient=0.10.0
+- nbconvert-core=7.16.4
+- nbformat=5.10.4
+- ncbi-amrfinderplus=3.12.8
+- ncbi-datasets-pylib=16.6.1
+- ncbi-vdb=3.1.1
+- ncurses=6.5
+- nest-asyncio=1.6.0
+- networkx=3.1
+- notebook=6.5.5
+- notebook-shim=0.2.4
+- numpy=1.26.4
+- oniguruma=6.9.9
+- openjdk=22.0.1
+- openjpeg=2.5.2
+- openssl=3.3.2
+- overrides=7.7.0
+- packaging=24.1
+- pandas=2.2.2
+- pandoc=3.5
+- pandocfilters=1.5.0
+- pango=1.54.0
+- paramiko=3.5.0
+- parsl=2024.4.15
+- parso=0.8.4
+- patsy=0.5.6
+- pcre2=10.43
+- perl=5.32.1
+- perl-archive-tar=2.40
+- perl-b-cow=0.007
+- perl-carp=1.50
+- perl-clone=0.46
+- perl-common-sense=3.75
+- perl-compress-raw-bzip2=2.201
+- perl-compress-raw-zlib=2.202
+- perl-config-general=2.65
+- perl-digest-perl-md5=1.9
+- perl-encode=3.21
+- perl-exporter=5.74
+- perl-exporter-tiny=1.002002
+- perl-extutils-config=0.008
+- perl-extutils-helpers=0.026
+- perl-extutils-installpaths=0.012
+- perl-extutils-makemaker=7.70
+- perl-extutils-pl2bat=0.005
+- perl-font-ttf=1.06
+- perl-gd=2.76
+- perl-inc-latest=0.500
+- perl-io-compress=2.201
+- perl-io-string=1.08
+- perl-io-zlib=1.14
+- perl-json=4.10
+- perl-json-xs=4.03
+- perl-list-moreutils=0.430
+- perl-list-moreutils-xs=0.430
+- perl-math-bezier=0.01
+- perl-math-round=0.07
+- perl-math-vecstat=0.08
+- perl-module-build=0.4234
+- perl-module-build-tiny=0.039
+- perl-module-implementation=0.09
+- perl-module-runtime=0.016
+- perl-number-format=1.76
+- perl-params-validate=1.31
+- perl-parent=0.241
+- perl-pathtools=3.75
+- perl-readonly=2.05
+- perl-regexp-common=2017060201
+- perl-scalar-list-utils=1.63
+- perl-set-intspan=1.19
+- perl-statistics-basic=1.6611
+- perl-storable=3.15
+- perl-svg=2.87
+- perl-test-fatal=0.016
+- perl-text-format=0.62
+- perl-time-hires=1.9764
+- perl-try-tiny=0.31
+- perl-types-serialiser=1.01
+- perl-xml-parser=2.44_01
+- pexpect=4.9.0
+- pickleshare=0.7.5
+- pillow=10.3.0
+- pip=24.2
+- pixman=0.43.4
+- pkgutil-resolve-name=1.3.10
+- platformdirs=4.3.6
+- pluggy=1.5.0
+- popt=1.16
+- prodigal-gv=2.11.0
+- prometheus_client=0.21.0
+- prompt-toolkit=3.0.48
+- protobuf=3.20.3
+- psutil=6.0.0
+- pthread-stubs=0.4
+- ptyprocess=0.7.0
+- pure_eval=0.2.3
+- pycparser=2.22
+- pyfaidx=0.8.1.3
+- pygments=2.18.0
+- pyhmmer=0.10.15
+- pyjwt=2.9.0
+- pynacl=1.5.0
+- pyobjc-core=10.3.1
+- pyobjc-framework-cocoa=10.3.1
+- pyparsing=3.2.0
+- pysam=0.22.1
+- pysocks=1.7.1
+- pytest=8.3.3
+- python=3.9.19
+- python-dateutil=2.8.2
+- python-fastjsonschema=2.20.0
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+- python_abi=3.9
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+- pyvcf3=1.0.3
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+- 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
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diff --git a/2024.10/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml b/2024.10/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml
new file mode 100644
index 00000000..bbad20f8
--- /dev/null
+++ b/2024.10/pathogenome/passed/qiime2-pathogenome-ubuntu-latest-conda.yml
@@ -0,0 +1,652 @@
+channels:
+- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed
+- conda-forge
+- bioconda
+dependencies:
+- _libgcc_mutex=0.1
+- _openmp_mutex=4.5
+- _r-mutex=1.0.1
+- alsa-lib=1.2.11
+- anyio=4.6.2.post1
+- appdirs=1.4.4
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+- argh=0.31.3
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+- arrow=1.3.0
+- asttokens=2.4.1
+- atpublic=5.0
+- attr=2.5.1
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+- bc=1.07.1
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+- bcrypt=4.2.0
+- beautifulsoup4=4.12.3
+- bedtools=2.31.1
+- bibtexparser=1.4.2
+- binutils_impl_linux-64=2.43
+- bioconductor-annotationdbi=1.64.1
+- bioconductor-biobase=2.62.0
+- bioconductor-biocfilecache=2.10.1
+- bioconductor-biocgenerics=0.48.1
+- bioconductor-biocio=1.12.0
+- bioconductor-biocparallel=1.36.0
+- bioconductor-biomart=2.58.0
+- bioconductor-biostrings=2.70.1
+- bioconductor-bsgenome=1.70.1
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+- bioconductor-s4vectors=0.40.2
+- bioconductor-sparsearray=1.2.2
+- bioconductor-structuralvariantannotation=1.18.0
+- bioconductor-summarizedexperiment=1.32.0
+- bioconductor-variantannotation=1.48.1
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+- pyqt5-sip=12.12.2
+- pysam=0.22.1
+- pysocks=1.7.1
+- pytest=8.3.3
+- python=3.9.19
+- python-dateutil=2.8.2
+- python-fastjsonschema=2.20.0
+- python-json-logger=2.0.7
+- python-tzdata=2024.2
+- python_abi=3.9
+- pytz=2024.2
+- 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+195.g9aef2fa
+- q2cli=2024.10.0.dev0+6.gfe7799f
+- q2templates=2024.10.0.dev0
+- qiime2=2024.10.0.dev0+17.g5fb10c4
+- qt-main=5.15.8
+- quast=5.2.0
+- r-abind=1.4_5
+- r-argparser=0.7.2
+- r-askpass=1.2.1
+- r-assertthat=0.2.1
+- r-backports=1.5.0
+- r-base=4.3.3
+- r-base64enc=0.1_3
+- r-bh=1.84.0_0
+- r-bit=4.5.0
+- r-bit64=4.5.2
+- r-bitops=1.0_9
+- r-blob=1.2.4
+- r-brio=1.1.5
+- r-broom=1.0.7
+- r-bslib=0.8.0
+- r-cachem=1.1.0
+- r-callr=3.7.6
+- r-cellranger=1.1.0
+- r-cli=3.6.3
+- r-clipr=0.8.0
+- r-codetools=0.2_20
+- r-colorspace=2.1_1
+- r-conflicted=1.2.0
+- r-cpp11=0.5.0
+- r-crayon=1.5.3
+- r-curl=5.2.1
+- r-data.table=1.15.2
+- r-dbi=1.2.3
+- r-dbplyr=2.5.0
+- r-desc=1.4.3
+- r-diffobj=0.3.5
+- r-digest=0.6.37
+- r-dplyr=1.1.4
+- r-dtplyr=1.3.1
+- r-ellipsis=0.3.2
+- r-evaluate=1.0.1
+- r-fansi=1.0.6
+- r-farver=2.1.2
+- r-fastmap=1.2.0
+- r-filelock=1.0.3
+- r-fontawesome=0.5.2
+- r-forcats=1.0.0
+- r-formatr=1.14
+- r-fs=1.6.4
+- r-futile.logger=1.4.3
+- r-futile.options=1.0.1
+- r-gargle=1.5.2
+- r-generics=0.1.3
+- r-getopt=1.20.4
+- r-ggplot2=3.5.1
+- r-glue=1.8.0
+- r-googledrive=2.1.1
+- r-googlesheets4=1.1.1
+- r-gtable=0.3.5
+- r-haven=2.5.4
+- r-here=1.0.1
+- r-highr=0.11
+- r-hms=1.1.3
+- r-htmltools=0.5.8.1
+- r-httr=1.4.7
+- r-ids=1.0.1
+- r-isoband=0.2.7
+- r-jquerylib=0.1.4
+- r-jsonlite=1.8.9
+- r-knitr=1.48
+- r-labeling=0.4.3
+- r-lambda.r=1.2.4
+- r-lattice=0.22_6
+- r-lifecycle=1.0.4
+- r-lubridate=1.9.3
+- r-magrittr=2.0.3
+- r-mass=7.3_60.0.1
+- r-matrix=1.6_5
+- r-matrixstats=1.4.1
+- r-memoise=2.0.1
+- r-mgcv=1.9_1
+- r-mime=0.12
+- r-modelr=0.1.11
+- r-munsell=0.5.1
+- r-nlme=3.1_165
+- r-openssl=2.2.2
+- r-optparse=1.7.5
+- r-pillar=1.9.0
+- r-pkgbuild=1.4.4
+- r-pkgconfig=2.0.3
+- r-pkgload=1.4.0
+- r-plogr=0.2.0
+- r-plyr=1.8.9
+- r-png=0.1_8
+- r-praise=1.0.0
+- r-prettyunits=1.2.0
+- r-processx=3.8.4
+- r-progress=1.2.3
+- r-ps=1.8.0
+- r-purrr=1.0.2
+- r-r6=2.5.1
+- r-ragg=1.3.3
+- r-rappdirs=0.3.3
+- r-rcolorbrewer=1.1_3
+- r-rcpp=1.0.13
+- r-rcpptoml=0.2.2
+- r-rcurl=1.98_1.16
+- r-readr=2.1.5
+- r-readxl=1.4.3
+- r-rematch=2.0.0
+- r-rematch2=2.1.2
+- r-reprex=2.1.1
+- r-reshape2=1.4.4
+- r-restfulr=0.0.15
+- r-reticulate=1.36.0
+- r-rjson=0.2.23
+- r-rlang=1.1.4
+- r-rmarkdown=2.28
+- r-rprojroot=2.0.4
+- r-rsqlite=2.3.7
+- r-rstudioapi=0.16.0
+- r-rvest=1.0.4
+- r-sass=0.4.9
+- r-scales=1.3.0
+- r-selectr=0.4_2
+- r-snow=0.4_4
+- r-stringdist=0.9.12
+- r-stringi=1.8.4
+- r-stringr=1.5.1
+- r-sys=3.4.3
+- r-systemfonts=1.1.0
+- r-testthat=3.2.1.1
+- r-textshaping=0.4.0
+- r-tibble=3.2.1
+- r-tidyr=1.3.1
+- r-tidyselect=1.2.1
+- r-tidyverse=2.0.0
+- r-timechange=0.3.0
+- r-tinytex=0.53
+- r-tzdb=0.4.0
+- r-utf8=1.2.4
+- r-uuid=1.2_1
+- r-vctrs=0.6.5
+- r-viridislite=0.4.2
+- r-vroom=1.6.5
+- r-waldo=0.5.3
+- r-withr=3.0.1
+- r-xfun=0.48
+- r-xml=3.99_0.17
+- r-xml2=1.3.6
+- r-yaml=2.3.10
+- readline=8.2
+- referencing=0.35.1
+- repeatmasker=4.1.7p1
+- requests=2.32.3
+- rescript=2024.10.0.dev0+24.g29bf18a
+- rfc3339-validator=0.1.4
+- rfc3986-validator=0.1.1
+- rmblast=2.14.1
+- rpds-py=0.20.0
+- rpsbproc=0.5.0
+- rsync=3.3.0
+- samtools=1.21
+- scikit-bio=0.6.0
+- scikit-learn=1.4.2
+- scipy=1.13.0
+- seaborn=0.12.2
+- seaborn-base=0.12.2
+- sed=4.8
+- send2trash=1.8.3
+- setproctitle=1.3.3
+- setuptools=75.1.0
+- shortuuid=1.0.13
+- simplejson=3.19.3
+- sip=6.7.12
+- six=1.16.0
+- sniffio=1.3.1
+- soupsieve=2.5
+- spades=3.15.2
+- stack_data=0.6.2
+- statsmodels=0.14.4
+- sysroot_linux-64=2.17
+- tar=1.34
+- tbb=2021.13.0
+- tblib=3.0.0
+- terminado=0.18.1
+- threadpoolctl=3.5.0
+- tinycss2=1.3.0
+- tk=8.6.13
+- tktable=2.10
+- toml=0.10.2
+- tomli=2.0.2
+- tomlkit=0.13.2
+- tornado=6.4.1
+- traitlets=5.9.0
+- trf=4.09.1
+- typeguard=4.3.0
+- types-python-dateutil=2.9.0.20241003
+- typing-extensions=4.12.2
+- typing_extensions=4.12.2
+- typing_utils=0.1.0
+- tzdata=2024b
+- tzlocal=2.1
+- unicodedata2=15.1.0
+- unifrac=1.3
+- unifrac-binaries=1.4
+- uri-template=1.3.0
+- urllib3=1.26.19
+- vsearch=2.22.1
+- wcwidth=0.2.13
+- webcolors=24.8.0
+- webencodings=0.5.1
+- websocket-client=1.8.0
+- wget=1.21.4
+- wheel=0.44.0
+- widgetsnbextension=4.0.13
+- xcb-util=0.4.0
+- xcb-util-image=0.4.0
+- xcb-util-keysyms=0.4.0
+- xcb-util-renderutil=0.3.9
+- xcb-util-wm=0.4.1
+- xkeyboard-config=2.42
+- xmltodict=0.14.2
+- xorg-fixesproto=5.0
+- xorg-inputproto=2.3.2
+- xorg-kbproto=1.0.7
+- xorg-libice=1.1.1
+- xorg-libsm=1.2.4
+- xorg-libx11=1.8.9
+- xorg-libxau=1.0.11
+- xorg-libxdmcp=1.1.5
+- xorg-libxext=1.3.4
+- xorg-libxfixes=5.0.3
+- xorg-libxi=1.7.10
+- xorg-libxrender=0.9.11
+- xorg-libxt=1.3.0
+- xorg-libxtst=1.2.5
+- xorg-recordproto=1.14.2
+- xorg-renderproto=0.11.1
+- xorg-xextproto=7.3.0
+- xorg-xf86vidmodeproto=2.3.1
+- xorg-xproto=7.0.31
+- xxhash=0.8.2
+- xz=5.2.6
+- yaml=0.2.5
+- yq=3.4.3
+- zeromq=4.3.5
+- zipp=3.20.2
+- zlib=1.2.13
+- zstd=1.5.6
diff --git a/2024.10/pathogenome/passed/seed-environment-conda.yml b/2024.10/pathogenome/passed/seed-environment-conda.yml
index 1fecc9b9..e79bbb4a 100644
--- a/2024.10/pathogenome/passed/seed-environment-conda.yml
+++ b/2024.10/pathogenome/passed/seed-environment-conda.yml
@@ -1,5 +1,5 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.10/metagenome/passed
+- https://packages.qiime2.org/qiime2/2024.10/pathogenome/passed
 - conda-forge
 - bioconda
 dependencies:
@@ -16,34 +16,32 @@ dependencies:
 - pysam=0.22.1
 - python=3.9.19
 - python_abi=3.9
-- q2-amrfinderplus=0.0.0
-- q2-assembly=2024.10.0.dev0
-- q2-demux=2024.10.0.dev0+2.gc13cafb
+- 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
+- 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+20.g30d8c74
-- q2-viromics=0.0.0
-- q2-vizard=2024.10.0.dev0
-- q2cli=2024.10.0.dev0+5.g76b8d1e
+- q2-types=2024.10.0.dev0+23.g4b9509a
+- q2-viromics=0+untagged.23.gc1af303
+- q2-vizard=2024.10.0.dev0+195.g9aef2fa
+- q2cli=2024.10.0.dev0+6.gfe7799f
 - q2templates=2024.10.0.dev0
-- qiime2=2024.10.0.dev0+12.g3581493
+- qiime2=2024.10.0.dev0+17.g5fb10c4
 - r-base=4.3.3
 - r-reticulate=1.36.0
-- rescript=2024.10.0.dev0+11.g4f7ab4b
+- rescript=2024.10.0.dev0+24.g29bf18a
 - scikit-bio=0.6.0
 - scikit-learn=1.4.2
 - scipy=1.13.0
 - seaborn=0.12.2
-# adding this dep to address feature-classifier test failure on osx
-# https://github.com/qiime2/distributions/actions/runs/11351275507/job/31639822132?pr=366#step:9:444
-- vsearch=2.22.1
 - unifrac-binaries=1.4
 - unifrac=1.3
+- vsearch=2.22.1
 extras:
   variant_override:
     qiime2_epoch: '2024.10'
diff --git a/2024.10/pathogenome/staged/seed-environment-conda.yml b/2024.10/pathogenome/staged/seed-environment-conda.yml
new file mode 100644
index 00000000..d253901a
--- /dev/null
+++ b/2024.10/pathogenome/staged/seed-environment-conda.yml
@@ -0,0 +1,47 @@
+channels:
+- https://packages.qiime2.org/qiime2/2024.10/pathogenome/staged
+- conda-forge
+- bioconda
+dependencies:
+- biom-format=2.1.15
+- bowtie2=2.5.1
+- h5py=3.11.0
+- hdf5=1.14.3
+- matplotlib=3.8.4
+- notebook=6.5.5
+- numpy=1.26.4
+- pandas=2.2.2
+- parsl=2024.4.15
+- patsy=0.5.6
+- 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+195.g9aef2fa
+- q2cli=2024.10.0.dev0+6.gfe7799f
+- q2templates=2024.10.0.dev0
+- qiime2=2024.10.0.dev0+17.g5fb10c4
+- r-base=4.3.3
+- r-reticulate=1.36.0
+- rescript=2024.10.0.dev0+24.g29bf18a
+- scikit-bio=0.6.0
+- scikit-learn=1.4.2
+- scipy=1.13.0
+- seaborn=0.12.2
+- unifrac-binaries=1.4
+- unifrac=1.3
+- vsearch=2.22.1
+extras:
+  variant_override:
+    qiime2_epoch: '2024.10'