REL: 2020.8

caporaso-lab · Oct 17, 2020 · 252e728 · 252e728
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -3,12 +3,12 @@ name: ci
 on:
   push:
     branches:
-      - master
+      - r2020.8
     paths-ignore:
       - 'conda-env-files/**'
   pull_request:
     branches:
-      - master
+      - r2020.8
 
 jobs:
   lint:
@@ -53,7 +53,7 @@ jobs:
 
   integrate:
     needs: build-and-test
-    if: github.ref == 'refs/heads/master'
+    if: github.ref == 'refs/heads/r2020.8'
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
@@ -87,7 +87,7 @@ jobs:
           source "$CONDA/etc/profile.d/conda.sh"
           sudo conda install -p ./genome-sampler-env -q \
             -c https://packages.qiime2.org/qiime2/unverified/ \
-            -c qiime2-staging \
+            -c qiime2 \
             -c conda-forge \
             -c bioconda \
             -c defaults \
@@ -111,7 +111,7 @@ jobs:
 
   commit-env-files:
     needs: integrate
-    if: github.ref == 'refs/heads/master'
+    if: github.ref == 'refs/heads/r2020.8'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -182,7 +182,7 @@ jobs:
     needs: doc-build
     runs-on: ubuntu-latest
     # TODO: update the following when cutting a release
-    if: github.ref == 'refs/heads/some-release-branch'
+    if: github.ref == 'refs/heads/r2020.8'
     steps:
     - name: fetch built docs
       uses: actions/download-artifact@v1

diff --git a/docs/downstream-workflows.md b/docs/downstream-workflows.md
@@ -33,8 +33,8 @@ haven't, you'll be missing files that are needed for this tutorial.
 ## Obtain reference sequence and alignment mask
 
 ```
-curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/snakemake/tutorial-data/alignment-mask.qza --output tutorial-data/alignment-mask.qza
-curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/snakemake/tutorial-data/sarscov2-reference-genome.qza --output tutorial-data/sarscov2-reference-genome.qza
+curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/snakemake/tutorial-data/alignment-mask.qza --output tutorial-data/alignment-mask.qza
+curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/snakemake/tutorial-data/sarscov2-reference-genome.qza --output tutorial-data/sarscov2-reference-genome.qza
 ```
 
 ## Align sequences and build a tree

diff --git a/docs/install.md b/docs/install.md
@@ -23,15 +23,15 @@ conda install wget
 For linux installation environments, please run:
 
 ```bash
-wget https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/conda-env-files/genome-sampler-py36-linux-conda.yml
+wget https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/conda-env-files/genome-sampler-py36-linux-conda.yml
 conda env create -n genome-sampler-2020.8 --file genome-sampler-py36-linux-conda.yml
 rm genome-sampler-py36-linux-conda.yml
 ```
 
 For macOS installation environments, please run:
 
 ```bash
-wget https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/conda-env-files/genome-sampler-py36-osx-conda.yml
+wget https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/conda-env-files/genome-sampler-py36-osx-conda.yml
 conda env create -n genome-sampler-2020.8 --file genome-sampler-py36-osx-conda.yml
 rm genome-sampler-py36-osx-conda.yml
 ```

diff --git a/docs/tutorial.md b/docs/tutorial.md
@@ -15,10 +15,10 @@ commands:
 
 ```
 mkdir -p tutorial-data
-curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/snakemake/tutorial-data/focal-seqs.fasta --output tutorial-data/focal-seqs.fasta
-curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/snakemake/tutorial-data/context-seqs.fasta --output tutorial-data/context-seqs.fasta
-curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/snakemake/tutorial-data/focal-metadata.tsv --output tutorial-data/focal-metadata.tsv
-curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/snakemake/tutorial-data/context-metadata.tsv --output tutorial-data/context-metadata.tsv
+curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/snakemake/tutorial-data/focal-seqs.fasta --output tutorial-data/focal-seqs.fasta
+curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/snakemake/tutorial-data/context-seqs.fasta --output tutorial-data/context-seqs.fasta
+curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/snakemake/tutorial-data/focal-metadata.tsv --output tutorial-data/focal-metadata.tsv
+curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/snakemake/tutorial-data/context-metadata.tsv --output tutorial-data/context-metadata.tsv
 ```
 
 ## Using `genome-sampler` (Snakemake workflow)
@@ -33,8 +33,8 @@ individually, move on to the next section.
 Download the Snakemake and associated config file using `curl` as follows:
 
 ```
-curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/snakemake/Snakefile --output Snakefile
-curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/master/snakemake/config.yaml --output config.yaml
+curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/snakemake/Snakefile --output Snakefile
+curl -sL https://raw.githubusercontent.com/caporaso-lab/genome-sampler/r2020.8/snakemake/config.yaml --output config.yaml
 ```
 
 Place the resulting Snakemake file in the same folder as the sequence and