update igraph packages

FredHutch · Oct 7, 2024 · eed949c · eed949c
1 parent 700c4a1
commit eed949c
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Showing 6 changed files with 337 additions and 123 deletions.
diff --git a/docs/bio-modules-18.04.md b/docs/bio-modules-18.04.md
diff --git a/docs/bio-modules-24.04.md b/docs/bio-modules-24.04.md
diff --git a/fh_easyconfigs/c/Cgl/Cgl-0.60.8-2023b.eb b/fh_easyconfigs/c/Cgl/Cgl-0.60.8-2023b.eb
@@ -30,14 +30,14 @@ dependencies = [
 ]
 
 # Use CoinUtils from EB
-configopts = '--with-coinutils-lib="-lCoinUtils" '
-configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data'
-# Use Clp from EB
-configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" '
-configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data'
-# Use Osi from EB (also needs links to Clp due to OsiClpSolver)
-configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" '
-configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data '
+configopts = ' '.join([
+    '--with-coinutils-lib="-lCoinUtils" ',
+    '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data',
+    '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ',
+    '--with-clp-datadir=$EBROOTCLP/share/coin/Data',
+    '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ',
+    '--with-osi-datadir=$EBROOTOSI/share/coin/Data ',
+])
 
 sanity_check_paths = {
     'files': ['lib/libCgl.%s' % SHLIB_EXT],

diff --git a/fh_easyconfigs/f/fhR/fhR-4.4.0-foss-2023b.eb b/fh_easyconfigs/f/fhR/fhR-4.4.0-foss-2023b.eb
@@ -28,15 +28,15 @@ dependencies = [
     # ('PostgreSQL', '15.2'),
     ('JAGS', '4.3.2'),
     ('GLPK', '5.0'), # rglpk
-    ('poppler', '24.03.0'), # pdftools
+    ('poppler', '24.04.0'), # pdftools
     ('Graphviz', '10.0.1'),
     ('NLopt', '2.7.1'),
     ('libGLU', '9.0.3'),
     ('ICU', '74.1'),
     ('netCDF', '4.9.2'),  # for netcdf4
     ('ZeroMQ', '4.3.5'),  # for zmq
     ('SYMPHONY', '5.7.2'), # for lpsymphony
-    ('igraph', '0.10.10'), # for igraph
+    ('igraph', '0.10.12'), # for igraph
     ('OpenJPEG', '2.5.0'),
     ('UnZip', '6.0'),
     ('NSS', '3.94'),

diff --git a/fh_easyconfigs/i/igraph/igraph-0.10.10-goff-2023b.eb b/fh_easyconfigs/i/igraph/igraph-0.10.10-goff-2023b.eb
diff --git a/scripts/create_module_list.sh b/scripts/create_module_list.sh
@@ -16,9 +16,8 @@ if [[ ! -z "${PWD##*${repo}*}" ]]; then
     exit 1
 fi
 
-# extract major.minor from OS relase: VERSION="16.04.3 LTS (Xenial Xerus)"
-os_ver=`grep '^VERSION=' /etc/os-release | sed 's/.*="\([0-9]*\.[0-9]*\).*$/\1/'`
-inventory=bio-modules-${os_ver}.md
+# get VERSION_ID from /etc/os-release 
+. /etc/os-release
 
 # remove the $repo from left everything else; add the $repo and the "/docs" dir back
 base_dir=${PWD%${repo}*}${repo}
@@ -31,15 +30,26 @@ module_dir=/app/modules
 
 echo Collecting Inventory
 cd $base_dir
-$spider -o spider-json ${module_dir}/bio:${module_dir}/math:${module_dir}/chem | python -mjson.tool >${docs_dir}/modules-${os_ver}.json
+moduleclass='ai bio chem math'
+module_search_path=''
+for class in $moduleclass; do
+   if [ -z $module_search_path ]; then
+       module_search_path=${module_dir}/${class}
+   else
+       module_search_path=${module_search_path}:${module_dir}/${class}
+   fi
+done
+echo $module_search_path
+$spider -o spider-json $module_search_path | python3 -mjson.tool > modules-${VERSION_ID}.json
+cp modules-${VERSION_ID}.json ${docs_dir} 
 
 echo Generating Markdown
-json_in=${docs_dir}/modules-${os_ver}.json
-md_file=bio-modules-${os_ver}
+json_in=${docs_dir}/modules-${VERSION_ID}.json
+md_file=bio-modules-${VERSION_ID}
 md_out=${docs_dir}/${md_file}.md
 
 echo '---' > ${md_out}
-echo 'title: Bio Modules' $os_ver >> ${md_out}
+echo 'title: Bio Modules' $VERSION_ID >> ${md_out}
 echo 'layout: single' >> ${md_out}
 echo "permalink: /${md_file}/" >> ${md_out}
 echo 'created: '`date +"%Y-%m-%d"` >> ${md_out}