merge with main

soybase · Nov 1, 2024 · f6324b6 · f6324b6
2 parents fcaeb73 + 7df64c3
commit f6324b6
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diff --git a/.github/workflows/build-deploy.yml b/.github/workflows/build-deploy.yml
@@ -53,7 +53,7 @@ jobs:
           cache-version: 0 # Increment this number if you need to re-download cached gems
       - name: Setup Pages
         id: pages
-        uses: actions/configure-pages@v4
+        uses: actions/configure-pages@v5
       - run: bundle exec jekyll build --profile --trace # --baseurl "${{ steps.pages.outputs.base_path }}" # sub-uri currently not supported by site
       - uses: actions/cache/restore@v4
         id: restore-cache-jbrowse
@@ -115,13 +115,13 @@ jobs:
           path: ./tmp/.htmlproofer
           key: html-proofer
       - name: run htmlproofer
-        continue-on-error: true
         # ignore HTTP status 301 (htmlproofer strips trailing slashes)
         run: |
           htmlproofer --allow-missing-href --ignore-missing-alt --ignore-files '/\/uikit\/tests\//' --ignore-status-codes '301,403,503' --cache '{"timeframe": {"external": "30d"}}' --ignore-url '/germplasm-map.legumeinfo.org/,/pgrc-rpc.agr.gc.ca\/gringlobal\/search/'
       # https://github.com/actions/cache/blob/main/save/README.md#always-save-cache
       - uses: actions/cache/save@v4
         id: save-cache-htmlproofer
+        if: always()
         with:
           path: ./tmp/.htmlproofer
           key: html-proofer

diff --git a/Makefile b/Makefile
@@ -1,12 +1,45 @@
+.POSIX:
+
+# USAGE
+#
+# 1. (macOS) Install XCode Developer Tools (if not already installed):
+#
+#     xcode-select --install
+#
+# 2. Create symbolic link to fix broken xcode ruby framework (first time only):
+#    Choose the appropriate target for your OS version: darwin22, darwin23, darwin24, etc.:
+#
+#   # macOS Sonoma (macOS 14):
+#      universal-darwin23 is missing in this MacOSX15.0.sdk, but universal-darwin24 is present, so link universal-darwin23 to universal-darwin24
+#      See https://stackoverflow.com/a/65481787 for discussion
+#
+#    sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/universal-darwin24 \
+#               /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/include/ruby-2.6.0/universal-darwin23
+#
+# 3.  Install dependencies (first time only, or until "make distclean" is invoked)
+#
+#     make install
+#
+# 4.  Start jekyll, listening on localhost:4000 (and livereload on default port 35729)
+#
+#     make
+#
+# 5. If generated site needs to be removed to pick up modifications made to
+#    _config.yml, plugin, _data, "etc."(?), run one of the following (see actions below)
+#
+#     make mostlyclean
+#  or
+#     make clean
+#
+
 OS = $(shell uname)
 ifeq ($(OS), Darwin)
-  # additional macOS environment variable needed at install time due to broken
-  # xcode ruby framework
-  export CPATH = /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.6/Headers/
   # install Ruby dependencies in $PWD/vendor
   export GEM_HOME=${PWD}/vendor/gems
   export PATH := ${PWD}/vendor/gems/bin:${PATH}
 
+  # select SDK from /Library/Developer/CommandLineTools/SDKs
+  XCRUN = DEVELOPER_DIR=/Library/Developer/CommandLineTools xcrun --sdk macosx15.0
   JEKYLL_SERVE_ARGS = --livereload
   HTMLPROOFER_ARGS = --allow-missing-href=true --ignore-missing-alt=true
   PYTHON_VENV_ACTIVATE = . ./vendor/python-venv/bin/activate
@@ -49,7 +82,7 @@ jbrowse: setup
 
 setup:
 	git submodule status | grep -q '^-' && git submodule update --init --recursive || true
-	if ! bundle check; then bundle install; fi
+	if ! bundle check; then $(XCRUN) bundle install; fi
 
 mostlyclean:
 	rm -rf .jekyll-cache/ .jekyll-metadata _site/

diff --git a/_data/projects.yml b/_data/projects.yml
@@ -41,7 +41,7 @@
         - name: information
           instances:
             - description: The list of soybean lines that have been resequenced (spreadsheet)
-              url: https://www.soybase.org/data/v2/Glycine/max/diversity/Wm82.gnm2.div.Valliyodan_Brown_2021/Wm82.gnm2.div.Valliyodan_Brown_2021USB481_accession_List.xlsx
+              url: https://data.soybase.org/Glycine/max/diversity//Wm82.gnm2.div.Valliyodan_Brown_2021/Wm82.gnm2.div.Valliyodan_Brown_2021USB481_accession_List.xlsx
     - category:
         - name: data
           instances:
@@ -214,15 +214,15 @@
             - description: "Data Store repository"
               url: "https://data.soybase.org/Glycine/max/diversity/Wm82.gnm2.div.Torkamaneh_Laroche_2019/"
             - description: "Download List of Accessions"
-              url: "https://www.soybase.org/data/v2/Glycine/max/diversity/Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.AccessionTable.txt.gz"
+              url: "https://data.soybase.org/Glycine/max/diversity//Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.AccessionTable.txt.gz"
             - description: "Download GmHapMap data in VCF format (1.9 GB compressed)"
-              url: "https://www.soybase.org/data/v2/Glycine/max/diversity/Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.SNPdata.vcf.gz"
+              url: "https://data.soybase.org/Glycine/max/diversity//Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.SNPdata.vcf.gz"
             - description: "Download Genotypes by Gene"
-              url: "https://www.soybase.org/data/v2/Glycine/max/diversity/Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.genotypes_by_gene.hmp.gz"
+              url: "https://data.soybase.org/Glycine/max/diversity//Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.genotypes_by_gene.hmp.gz"
             - description: "Download Haplotypes by Gene"
-              url: "https://www.soybase.org/data/v2/Glycine/max/diversity/Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.haplotypes_by_gene.tsv.gz"
+              url: "https://data.soybase.org/Glycine/max/diversity//Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.haplotypes_by_gene.tsv.gz"
             - description: "Download Loss of Function SNPs"
-              url: "https://www.soybase.org/data/v2/Glycine/max/diversity/Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.loss_of_function.xlsx.gz"
+              url: "https://data.soybase.org/Glycine/max/diversity//Wm82.gnm2.div.Torkamaneh_Laroche_2019/glyma.Wm82.gnm2.div.Torkamaneh_Laroche_2019.loss_of_function.xlsx.gz"
 
 -
   DataStoreID: "Wang_Chu_2016"
@@ -531,11 +531,11 @@
             - description: "Predicted genes from the PanSoy genomic data, file PanSoy_genes_not_in_Wm82.fna. This includes both genes identified in Wm82.gnm4 and genes in the PanSoy complement."
               url: "https://data.soybase.org/Glycine/max/pangenomes/Wm82.gnm4.pan.W46N/glyma.Wm82.gnm4.pan.W46N.PanSoy.ptpg.gtf.gz"
             - description: "Coding sequence (CDS) predicted from the PanSoy genomic sequence, not in Wm84.gnm4."
-              url: "https://www.soybase.org/data/v2/Glycine/max/pangenomes/Wm82.gnm4.pan.W46N/glyma.Wm82.gnm4.pan.W46N.PanSoy_cds_not_in_Wm82.fna.gz"
+              url: "https://data.soybase.org/Glycine/max/pangenomes/Wm82.gnm4.pan.W46N/glyma.Wm82.gnm4.pan.W46N.PanSoy_cds_not_in_Wm82.fna.gz"
             - description: "The PanSoy genomic sequence, present in one or more of the 204 accessions described in Torkamaneh, Lemay, Belzile (2021) but not in the reference Wm82.gnm4."
-              url: "https://www.soybase.org/data/v2/Glycine/max/pangenomes/Wm82.gnm4.pan.W46N/glyma.Wm82.gnm4.pan.W46N.PanSoy_seq_not_in_Wm82.fna.gz"
+              url: "https://data.soybase.org/Glycine/max/pangenomes/Wm82.gnm4.pan.W46N/glyma.Wm82.gnm4.pan.W46N.PanSoy_seq_not_in_Wm82.fna.gz"
             - description: "Supplementary tables S1-S7 from Torkamaneh, Lemay, Belzile (2021), including gene presence-absence variation for genes predicted in Wm82.gnm4.ann1 and in the 204 accessions described in this study."
-              url: "https://www.soybase.org/data/v2/Glycine/max/pangenomes/Wm82.gnm4.pan.W46N/glyma.Wm82.gnm4.pan.W46N.PanSoy_supp_tables.xlsx"
+              url: "https://data.soybase.org/Glycine/max/pangenomes/Wm82.gnm4.pan.W46N/glyma.Wm82.gnm4.pan.W46N.PanSoy_supp_tables.xlsx"
 -
   DataStoreID: "Espina_Ahmed_2018"
   short_title: "Soybean EMS Mutagenized Population"
@@ -806,3 +806,4 @@
               url: "https://legacy.soybase.org/gb2/gbrowse/gmax1.01?label=Wm82_potential_SSR"
             - description: "Wm82 Potential SSR on assembly version 2"
               url: "https://legacy.soybase.org/gb2/gbrowse/gmax2.0?label=wm82_potential_ssr"
+
diff --git a/about/soybase_about/index.html b/about/soybase_about/index.html
@@ -11,7 +11,7 @@ <h3>About the SoyBase database and soybeans</h3>
 
 <p>The SoyBase</a> database was established in the 1990s as the <a href="https://www.usda.gov">USDA</a> Soybean Genetics Database. Originally, it contained only genetic information about soybeans such as genetic maps and information about the Mendelian genetics of soybean. In time SoyBase was expanded to include molecular data regarding soybean genes and sequences as they became available. In 2010, the soybean genome sequence was published and it and supporting gene sequences have been integrated into the SoyBase <a href="/resources">sequence browsers</a>. SoyBase genetic maps were used in the assembly of both the Williams 82 reference genome assemblies.</p>
 
-<p>SoyBase also incorporates information about <a href="https://www.soybase.org/mutants/">mutant</a> and other soybean genetic stocks and serves as a contact point for ordering strains from those populations. As association analyses continue due to various re-sequencing efforts SoyBase will also incorporate those data into the soybean <a href="{% link tools/browsers/index.html %}">genome browser</a> as they become available. Gene expression patterns are also available at SoyBase through the SoyBase expression pages and the Soybean Gene <a href="https://www.soybase.org/soyseq/">Atlas</a>. Other expression/transcriptome/methylomic data sets also have been and continue to be incorporated into the SoyBase genome browser.</p>
+<p>SoyBase also incorporates information about <a href="https://legacy.soybase.org/mutants/">mutant</a> and other soybean genetic stocks and serves as a contact point for ordering strains from those populations. As association analyses continue due to various re-sequencing efforts SoyBase will also incorporate those data into the soybean <a href="{% link tools/browsers/index.html %}">genome browser</a> as they become available. Gene expression patterns are also available at SoyBase via the <a href="/tools/expression"><b>Expression resources</b></a> page.</p>
 
 <div style="width:300px;float:right;margin:10px;border:1px solid darkgreen;">
   <img src="/assets/img/general/soybean2.jpg" alt="Image: Mature soybean plant"/>

diff --git a/events/_posts/2022-06-03-Soy2022.md b/events/_posts/2022-06-03-Soy2022.md
@@ -6,7 +6,5 @@ end_date: 2022-08-23
 summary: Molecular and Cellular Biology of the Soybean (Soy2022) 22-23 August, 2022
 ---
 22 - 23 August 2022:<br>
-Registration for Virtual Soy2022 is now OPEN! <br>
-[Meeting website](https://www.regcytes.extension.iastate.edu/soy2022/); <br>
-[Registration page](https://www.regcytes.extension.iastate.edu/soy2022/register/).
+Registration for Virtual Soy2022 has closed. <br>
 
diff --git a/tools/translate/index.html b/tools/translate/index.html
@@ -141,7 +141,7 @@ <h2>Gene Model Translation / Correspondence</h2>
           <li>glyma.Wm82.gnm5.ann1</li>
           <li>glyma.Wm82.gnm6.ann1</li>
           <li>glyma.Wm82_IGA1008.gnm1.ann1</li>
-          <li>glyma.Wm82_ISU01.gnm2.ann1</li>
+          <li>glyma.Wm82.gnm6.ann1</li>
           <li>glyma.Wm82_NJAU.gnm1.ann1</li>
           <li>glyma.XuDouNo_1.gnm1.ann1</li>
           <li>glyma.YuDouNo_22.gnm1.ann1</li>