Merge pull request #12 from LadnerLab/adding-psea-docs

Adding psea docs

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:
@@ -61,8 +64,17 @@ 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 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
         working-directory: ${{ github.workspace }}/main/source

.github/workflows/test_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:
@@ -61,8 +64,24 @@ 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: Verify QIIME 2 Install
+        working-directory: ${{ github.workspace }}/main
+        run: |
+          source "$CONDA/etc/profile.d/conda.sh"
+          conda activate ./test-env
+          qiime info
+
+      - 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
         working-directory: ${{ github.workspace }}/main/source

install_r_packages.R

@@ -0,0 +1,18 @@
+# Please note there is also a package via Anaconda: https://anaconda.org/bioconda/bioconductor-clusterprofiler
+# Additionally, please be aware you may want to have a dedicated environment if
+# you install via Anaconda because of conflicts with various dependencies
+
+# Install igraph: https://github.com/igraph/rigraph
+options(
+  repos = c(
+    igraph = 'https://igraph.r-universe.dev',
+    CRAN = 'https://cloud.r-project.org'
+  )
+)
+install.packages('igraph')
+
+# Installation instructions for Bioconductor: https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#installing-biocmanager
+install.packages("BiocManager", repos = "https://cloud.r-project.org")
+
+BiocManager::install()  # update Bioconductor packages
+BiocManager::install("clusterProfiler", force=TRUE)

qiime2-2023.7-py38-linux-conda.yml

@@ -45,10 +45,12 @@ 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
@@ -410,6 +412,7 @@ dependencies:
 - r-beeswarm=0.4.0
 - r-bh=1.81.0_1
 - r-bibtex=0.5.1
+- r-biocmanager=1.30.22
 - r-bit=4.0.5
 - r-bit64=4.0.5
 - r-bitops=1.0_7
@@ -449,6 +452,7 @@ dependencies:
 - r-ellipsis=0.3.2
 - r-emmeans=1.8.8
 - r-energy=1.7_11
+- r-essentials=4.2
 - r-estimability=1.4.1
 - r-evaluate=0.21
 - r-exact=3.2
@@ -472,7 +476,9 @@ dependencies:
 - r-generics=0.1.3
 - r-getopt=1.20.3
 - r-ggbeeswarm=0.7.2
+- r-ggforce=0.4.2
 - 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
@@ -579,11 +585,13 @@ dependencies:
 - r-rvest=1.0.3
 - r-sass=0.4.7
 - r-scales=1.2.1
+- r-scatterpie=0.2.2
 - 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
@@ -621,6 +629,7 @@ 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

requirements.txt

@@ -13,3 +13,4 @@ q2-autopepsirf @ git+https://github.com/LadnerLab/q2-autopepsirf@main
 q2-pepsirf @ git+https://github.com/LadnerLab/q2-pepsirf@sync-deconv-ISS161
 q2-ps-plot @ git+https://github.com/LadnerLab/q2-ps-plot@upgrade-altair-v5
 q2-ps-qc @ git+https://github.com/LadnerLab/q2-ps-qc@main
+q2-PSEA @ git+https://github.com/LadnerLab/q2-PSEA@main

source/Pepsirf_Plugins/index.rst

@@ -8,3 +8,4 @@ Installation
    q2-ps-plot
    q2-ps-qc
    q2-autopepsirf
+   q2-PSEA

source/Pepsirf_Plugins/q2-PSEA.rst

@@ -0,0 +1,86 @@
+q2-PSEA
+=======
+
+Qiime2 plugin used to accomplish Peptide Set Enrichment Analysis (PSEA) and
+visualize results.
+
+Installation
+------------
+
+
+Dependencies:
+`````````````
+
+- ``qiime2-2023.7 or later``
+- ``q2-pepsirf``
+- ``q2-ps-plot``
+- ``altair v5.0.0 or later``
+- ``altair_saver v0.5.0 or later``
+- ``rpy2 v3.5.11 or later``
+
+R Dependencies:
+```````````````
+
+- ``r-base v4.2.2 or later``
+- ``r-biocmanager``
+- ``r-essentials v1.7.0 or later``
+- ``r-igraph v1.4.2 or later``
+- ``r-ggraph v2.1.0 or later``
+- ``r-ggforce v0.4.1 or later``
+- ``r-scatterpie v0.2.1 or later``
+- ``r-splines2 v0.5.1 or later``
+- ``bioconductor-ggtree v3.6.0 or later``
+- ``bioconductor-enrichplot v1.18.0 or later``
+
+Qiime2 Installation:
+````````````````````
+
+Visit: https://docs.qiime2.org/2022.2/install/ for intallation documentation on Qiime2
+
+
+q2-pepsirf Installation:
+````````````````````````
+
+Visit: https://ladnerlab.github.io/pepsirf-q2-plugin-docs/Pepsirf_Plugins/q2-pepsirf1/ 
+for installation documentation on q2-pepsirf
+
+
+q2-ps-plot Installation:
+`````````````````````````
+
+Visit: https://ladnerlab.github.io/pepsirf-q2-plugin-docs/Pepsirf_Plugins/q2-ps-plot/ 
+for installation documentation on q2-ps-plot
+
+
+q2-PSEA Installation:
+`````````````````````
+
+Make sure your Qiime2 conda environment is activated by running the command: 
+
+``conda activate qiime2-2023.7``
+
+You can replace qiime2-2023.7 above with whichever version of QIIME 2 you have currently installed.
+
+To help make installing R dependencies easier, please use this command if you have trouble:
+``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``
+
+You will need to install clusterProfiler through R to avoid conflicting versions with some packages:
+Please download the custom R script to do so here: https://github.com/LadnerLab/q2-PSEA/blob/main/install_r_packages.R
+``Rscript path/to/install_r_packages.R``
+``rm path/to/install_r_packages.R``
+
+Now you are ready to install q2-PSEA. Run the following commands:
+
+``pip install git+https://github.com/LadnerLab/q2-PSEA.git``
+
+Run qiime info to check for a successful installation. If installation was successful, you should see psea: version in the list of installed plugins.
+
+Using provided example data, average run time for 3 trials was: 1 Minute 21 Seconds
+
+Updating
+--------
+
+To update q2-PSEA, run the following command:
+
+``pip install -U git+https://github.com/LadnerLab/q2-PSEA.git``

source/Pepsirf_Plugins/q2-autopepsirf.rst

@@ -61,6 +61,6 @@ Typical Run Time: 4.43 Seconds
 Updating
 --------
 
-To update q2-pepsirf, run the following command:
+To update q2-autopepsirf, run the following command:
 
 ``pip install -U git+https://github.com/LadnerLab/q2-autopepsirf.git``