Fixed a couple bugs in PSEA tutorial. Redownloaded a fresh qiime2 env file, and updated docs workflows so clusterProfiler dependencies get installed the recommended way which is outlined in the installation instructions for q2-PSEA.

Author: Num0Programmer

.github/workflows/build_docs.yml

@@ -46,6 +46,9 @@ jobs:
         with:
           python-version: 3.8
 
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
       # Checkout the main branch (docs will be built from this)
       - uses: actions/checkout@v2
         with:
@@ -61,7 +64,6 @@ jobs:
         run: |
           # version should change as plugins are updated in accordance to qiime2 version (as needed)
           envFile=qiime2-2023.7-py38-linux-conda.yml
-          # wget https://raw.githubusercontent.com/qiime2/environment-files/master/2023.7/release/$envFile
           conda env create -q -p ./test-env --file $envFile
 
       - name: Install R requirements
@@ -70,6 +72,17 @@ jobs:
         run: |
           source "$CONDA/etc/profile.d/conda.sh"
           conda activate ../test-env
+          conda install -c conda-forge r-base r-essentials r-igraph r-ggraph r-ggforce r-scatterpie rpy2 r-biocmanager r-splines2
+          conda install -c bioconda bioconductor-ggtree bioconductor-enrichplot
+
+      - name: Install clusterProfiler package
+        working-directory: ${{ github.workspace }}/main
+        shell: bash -l {0}
+        run: |
+          which Rscript
+          source "$CONDA/etc/profile.d/conda.sh"
+          conda activate ../test-env
+          # TODO: update install_r_packages.R as needed
           Rscript install_r_packages.R
           
       - name: Install Sphinx requirements

.github/workflows/test_docs.yml

@@ -64,16 +64,25 @@ jobs:
         run: |
           # version should change as plugins are updated in accordance to qiime2 version (as needed)
           envFile=qiime2-2023.7-py38-linux-conda.yml
-          # wget https://raw.githubusercontent.com/qiime2/environment-files/master/2023.7/release/$envFile
           conda env create -q -p ./test-env --file $envFile
 
       - name: Install R requirements
+        working-directory: ${{ github.workspace }}/main
+        shell: bash -l {0}
+        run: |
+          source "$CONDA/etc/profile.d/conda.sh"
+          conda activate ../test-env
+          conda install -c conda-forge r-base r-essentials r-igraph r-ggraph r-ggforce r-scatterpie rpy2 r-biocmanager r-splines2
+          conda install -c bioconda bioconductor-ggtree bioconductor-enrichplot
+
+      - name: Install clusterProfiler package
         working-directory: ${{ github.workspace }}/main
         shell: bash -l {0}
         run: |
           which Rscript
           source "$CONDA/etc/profile.d/conda.sh"
           conda activate ../test-env
+          # TODO: update install_r_packages.R as needed
           Rscript install_r_packages.R
           
       - name: Install Sphinx requirements

qiime2-2023.7-py38-linux-conda.yml

@@ -9,7 +9,6 @@ dependencies:
 - _r-mutex=1.0.1
 - alsa-lib=1.2.8
 - altair=5.0.1
-- altair_saver=0.5.0
 - anyio=3.7.1
 - appdirs=1.4.4
 - argcomplete=3.1.1
@@ -45,12 +44,10 @@ dependencies:
 - bioconductor-delayedarray=0.24.0
 - bioconductor-delayedmatrixstats=1.20.0
 - bioconductor-dirichletmultinomial=1.40.0
-- bioconductor-enrichplot=1.18.0
 - bioconductor-genomeinfodb=1.34.9
 - bioconductor-genomeinfodbdata=1.2.9
 - bioconductor-genomicalignments=1.34.0
 - bioconductor-genomicranges=1.50.0
-- bioconductor-ggtree=3.6.0
 - bioconductor-iranges=2.32.0
 - bioconductor-matrixgenerics=1.10.0
 - bioconductor-mia=1.6.0
@@ -412,7 +409,6 @@ dependencies:
 - r-beeswarm=0.4.0
 - r-bh=1.81.0_1
 - r-bibtex=0.5.1
-- r-biocmanager
 - r-bit=4.0.5
 - r-bit64=4.0.5
 - r-bitops=1.0_7
@@ -452,7 +448,6 @@ dependencies:
 - r-ellipsis=0.3.2
 - r-emmeans=1.8.8
 - r-energy=1.7_11
-- r-essentials=1.7.0
 - r-estimability=1.4.1
 - r-evaluate=0.21
 - r-exact=3.2
@@ -476,9 +471,7 @@ dependencies:
 - r-generics=0.1.3
 - r-getopt=1.20.3
 - r-ggbeeswarm=0.7.2
-- r-ggforce=0.4.1
 - r-ggplot2=3.4.3
-- r-ggraph=2.1.0
 - r-ggrastr=1.0.2
 - r-ggrepel=0.9.3
 - r-gld=2.6.6
@@ -585,13 +578,11 @@ dependencies:
 - r-rvest=1.0.3
 - r-sass=0.4.7
 - r-scales=1.2.1
-- r-scatterpie=0.2.1
 - r-scs=3.2.4
 - r-selectr=0.4_2
 - r-sitmo=2.0.2
 - r-snow=0.4_4
 - r-sp=2.0_0
-- r-splines2=0.5.1
 - r-statmod=1.5.0
 - r-stringi=1.7.12
 - r-stringr=1.5.0
@@ -629,15 +620,13 @@ dependencies:
 - rfc3339-validator=0.1.4
 - rfc3986-validator=0.1.1
 - rpds-py=0.10.0
-- rpy2=3.5.11
 - samtools=1.17
 - scikit-bio=0.5.8
 - scikit-learn=0.24.1
 - scipy=1.10.0
 - seaborn=0.12.2
 - seaborn-base=0.12.2
 - sed=4.8
-- selenium=4.2.0
 - send2trash=1.8.2
 - sepp=4.3.10
 - setproctitle=1.3.2

source/tutorials/index.rst

@@ -9,3 +9,4 @@ Tutorials
    ps-plot
    ps-qc
    pepsirf
+   psea

source/tutorials/q2-PSEA.rst renamed to source/tutorials/psea.rst

@@ -35,20 +35,19 @@ Here we will test q2-PSEA's generate-vis module by running the following command
 
 	scatter_plot, volcano_plot = use.action(
 		use.UsageAction(
-			plugin_id="q2_PSEA",
-			action_id="generate_vis"
+			plugin_id="psea",
+			action_id="make_psea_table"
 		),
 		use.UsageInputs(
 			scores_file="source/data/IM0031_PV2T_25nt_raw_2mm_i1mm_Z-HDI75.tsv",
 			pairs_file="source/data/pairs.tsv",
 			peptide_sets_file="source/data/input.gmt",
-			theshold=0.750000,
+			threshold=0.750000,
 			species_taxa_file="source/data/species_taxa.tsv",
 			min_size=3,
 			max_size=5000,
 			permutation_num=10000,
-			table_dir="psea-example-tables",
-	        pepsirf_binary = "/home/runner/work/pepsirf-q2-plugin-docs/pepsirf-q2-plugin-docs/pepsirf"
+			table_dir="psea-example-tables"
 		),
 		use.UsageOutputNames(
 			scatter_plot="scatter_plot",