Cellphy install for INC1508101

easyconfigs/c/Cellphy/Cellphy-0.9.2-foss-2022b.eb

@@ -0,0 +1,34 @@
+#
+easyblock = 'Tarball'
+
+name = 'Cellphy'
+version = '0.9.2'
+
+homepage = 'https://github.com/amkozlov/cellphy'
+description = """CellPhy: accurate and fast probabilistic inference of single-cell phylogenies"""
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/amkozlov/cellphy/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+patches = ['Cellphy_modify_paths.patch']
+checksums = [
+    {'v0.9.2.tar.gz': 'dd9b4066c92ab387fcfbd53cdb29594e3f8be94ebcb48470206babd1597856b4'},
+    {'Cellphy_modify_paths.patch': '21203a9b3c5b10c3cf4441cfd620258042490694d643459a1ca487e260038993'},
+]
+
+dependencies = [
+    ('R', '4.3.1'),
+    ('R-bundle-Bioconductor', '3.17', '-R-%(rver)s'),
+    ('BCFtools', '1.17'),
+]
+
+postinstallcmds = ["ln -s %(installdir)s/cellphy.sh %(installdir)s/bin/cellphy"]
+
+modloadmsg = """Do `cellphy -h` for options"""
+
+sanity_check_paths = {
+    'files': ['bin/cellphy'],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'bio'

easyconfigs/c/Cellphy/Cellphy_modify_paths.patch

@@ -0,0 +1,31 @@
+--- cellphy.sh.old	2024-07-24 18:40:12.731667434 +0100
++++ cellphy.sh	2024-07-24 18:42:26.250453987 +0100
+@@ -11,7 +11,7 @@
+
+ usage() 
+ {
+-  echo "Usage: ./cellphy.sh [COMMAND] [options] input.VCF"
++  echo "Usage: cellphy [COMMAND] [options] input.VCF"
+   echo "\nCOMMAND:"
+   echo "\tFULL         Tree search+bootstrapping+mutation mapping (default)"
+   echo "\tSEARCH       Thorough tree search (20 starting trees) "
+@@ -25,7 +25,7 @@
+   echo "\t-r           REDO mode: overwrite all result files"
+   echo "\t-t THREADS   Number of threads to use (default: autodetect)"
+
+-  echo "\nExpert usage: ./cellphy.sh RAXML [raxml options]\n"
++  echo "\nExpert usage: cellphy RAXML [raxml options]\n"
+ }
+
+ version
+@@ -35,8 +35,8 @@
+   exit 1
+ fi
+
+-root=`dirname $0`
+-raxml_stem=$root/bin/raxml-ng-cellphy
++root=$EBROOTCELLPHY
++raxml_stem=raxml-ng-cellphy
+ sc_convert=$root/script/sc-caller-convert.sh
+ support_viz=$root/script/support-map.R
+ mutmap_viz=$root/script/mutation-map.R